The 31-year-old, top scorer in Germany's top-flight this season with 14 goals, was taken off in the first half of the 1-1 draw at Dortmund.
Kane has also had the most shots of any player in the Bundesliga (46, level with Omar Marmoush), and had the most big chances (17, scoring 10).
"Kane suffered a small muscle tear in the back of his right thigh," the club said in a statement. "Which means Bayern will have to do without Kane for the time being."
Bayern manager Vincent Kompany admitted Kane was unlikely to be fit to face Bayer Leverkusen, who they host in the DFB-Pokal round of 16 on Tuesday.
"Obviously, it will be tight for Tuesday. I don't know many players who can recover that quickly," Kompany said after the Dortmund game.
German media reported that the England captain could be sidelined for at least two weeks. Bundesliga leaders Bayern host Heidenheim on Saturday.
Hansi Flick's team won a Bundesliga, DFB-Pokal and Champions League treble in 2019-20, seeing off Paris Saint-Germain in the final of the European football's premier competition in August.
Robert Lewandowski and Joshua Kimmich were the only Bayern players to make the long-list last year, and those two again feature this time around.
Lewandowski scored a remarkable 55 goals across all competitions for Bayern last term, and has hit the ground running this season, netting 15 times to take his tally for the year so far to 70.
Manuel Neuer enjoyed something of a resurgence last term and heads up a list of 10 goalkeepers.
David Alaba was last on the list in 2017 but returns after starring at centre-back alongside Jerome Boateng, who also makes his first appearance in three years.
Thomas Muller is back after a four-year absence, while Alphonso Davies, Serge Gnabry and Leon Goretzka are all included for the first time.
Philippe Coutinho was something of a bit-part player though did score twice and provide an assist in a thumping 8-2 win over Barcelona – where he has now returned after a loan spell in Munich – in the Champions League semi-finals, while Thiago Alcantara, now of Liverpool, also features.
The list, which is based on players who received the most votes from other professionals, also includes 11 new faces.
It is no shock to see Borussia Dortmund's scoring sensation Erling Haaland make the cut, while Manchester United playmaker Bruno Fernandes is also involved.
Dele Alli, meanwhile, is something of a surprise inclusion.
The Tottenham midfielder has fallen out of favour under Jose Mourinho, making only two Premier League appearances, with his only top-flight start coming in the opening day defeat to Everton – in total, Alli has played just 66 league minutes this term.
Premier League champions Liverpool have eight players on the list, including new signing Thiago.
Lionel Messi and Cristiano Ronaldo are included among 15 forwards, while Dani Alves is the only player on the list not to play in Europe's top five leagues.
The 2020 FIFA FIFPRO Men's World 11 will be made up of the goalkeeper, three defenders, three midfielders and three attackers who receive the most votes, with the final spot going to the highest-ranking outfielder outside of the top nine.
The Bundesliga champions have already signed big-name duo Sadio Mane and Matthijs de Ligt, while the promising Ryan Gravenberch and Noussair Mazraoui have arrived from Ajax.
Speaking at a news conference to present De Ligt to the media after his €80million arrival from Juventus, Kahn revealed he expects there to be further movement.
Teenage Rennes forward Tel, experienced RB Leipzig midfielder Laimer and Germany international Raum have all been linked with a switch to the Allianz Arena.
"We have had further discussions with these players and now we just have to wait and see," said Bayern CEO Kahn on Wednesday.
"The transfer window is still open for a while. Sometimes things move very quickly.
"After analysing last season, we thought we should make a few statements. We want to continue to be among the top four teams in Europe."
Bayern have lost star striker Robert Lewandowski to Barcelona, with the Catalan giants continuing to make significant outlays in the transfer market despite questions about their finances.
Julian Nagelsmann openly questioned the situation at Barca but Kahn was far more cautious on the subject.
"You can't be fooled by all the transfers from Barcelona. I'm not a fan of judging things from the outside," said Kahn.
"None of us can really judge how the situation is. I find that a bit difficult. They'll know what they're doing because they're the only ones who really know the numbers."
That is according to Bayern chief executive Jan-Christian Dreesen, who discussed the club's squad-building plans in an interview with German outlet Abendzeitung.
Wirtz has attracted interest from a host of Europe's biggest clubs after helping Leverkusen to an unbeaten title triumph in 2023-24, winning the Bundesliga's Player of the Season award after scoring 11 goals and providing 11 assists in the competition.
Wirtz has four goals and two assists in the league so far this term, while only Alex Grimaldo (35) and Kevin Stoger (33) have bettered his 26 chances created in the Bundesliga and his figure of 3.9 expected assists (xA) puts him second to Grimaldo (4.22).
Bayern's tendency to swoop for Germany's brightest and best has led to them being linked with Wirtz, but Dreesen says finances will dictate their ability to make a move.
"It must always be in Bayern's interest to have the best German players with them," he said.
"But it is also true that Uli Hoeness always said Bayern must act in an economically sensible way. He would not agree with us if we did not observe both of his fundamental pillars."
Since the start of last season, Wirtz leads all players in the Bundesliga for successful dribbles, with 112. Second by that metric by Musiala, who has completed 109 for Bayern in that time.
Bayern are set to open talks over a new deal with the attacking midfielder, whose current deal with the Bavarian giants expires in 2026.
"It's no news that we naturally want to extend with one of the top players in the world who is in our ranks," Dreesen said.
"Jamal Musiala has developed excellently with us, he is a player who inspires the crowd, who creates a spectacle due to his individual class, who can turn a game around.
"I very much hope that these first really good talks that Max Eberl and Christoph Freund have with Jamal will ultimately lead to an extension.
"I don't want to put this in a corset in terms of time. The important thing is that it comes to that, even if it doesn't happen by the end of the year. Jamal Musiala is one of the faces of the future for FC Bayern."
Dreesen is also keen to see Joshua Kimmich put pen to paper on a new contract, with the midfielder having less than a year to run on his current deal.
"Joshua, who has a high degree of sporting ambition, knows which club he is in and what goals he can achieve here together with us," Dreesen said.
"He feels comfortable in Munich and is a very important player in this team.
"We have already said publicly that we now want to start talks with him about a contract extension quickly."
The league leaders will be without midfielder Joao Palhinha and forward Mathys Tel, who picked up injuries on international duty with Portugal and France respectively, while goalkeeper Manuel Neuer is nursing a ribcage injury and is racing to be fit.
Bayern have a busy schedule coming up after facing Augsburg, with a Champions League game at home to Paris Saint-Germain on Tuesday before the trip to Borussia Dortmund in the Bundesliga in just over a week.
They cap off their 11-day four-match run with the DFB-Pokal last-16 clash at home to holders Bayer Leverkusen on 3 December.
"We are missing Palhinha and Mathys Tel also got a knock while with the national team," Kompany told a press conference on Thursday. "The one fear we have as coach is for players to leave and come back injured.
"We are playing against Augsburg. It is important that it is only about the next game. We want to deliver the performance as we did before the international break. It is only about Augsburg and only this step is important for me today."
Kompany is in his first season in charge but knows expectations are high, and the team must remain contenders in all three competitions going into the new year.
"We're satisfied with the season we've played so far in all competitions despite the two defeats in the Champions League," said Bayern sports director Max Eberl, referring to their 1-0 defeat away to Aston Villa and 4-1 loss at Barcelona.
"It is a new format and we're still getting to know it," he added, with Bayern down in 17th place in the play-off spots.
"We have PSG which is a special game, Leverkusen in the Cup and Dortmund in the league. We want to start and win every single game. That is our starting point."
Leverkusen won their first domestic double last term but Bayern, desperate to restore their national dominance, are undefeated in the Bundesliga and have quickly carved out a five-point lead at the top over second-placed RB Leipzig.
The Bavarians have 26 points, with Leverkusen, who host Heidenheim on Saturday, nine behind in fourth. Dortmund welcome Freiburg, having dropped to seventh spot on 16 points, while Leipzig travel to Hoffenheim.
Bayern earned a much-needed victory in the Champions League in midweek, beating Paris Saint-Germain 1-0 to move up to 13th place in the new 36-team standings.
Kompany's side have also impressed in the Bundesliga, sitting six points clear at the summit following Harry Kane's hat-trick in their 3-0 triumph over Augsburg last time out.
The Belgian boss has collected 29 points in his first 11 Bundesliga games as a coach, equalling the league record only previously achieved by Pep Guardiola with Bayern in 2012-13 and by Klaus Toppmoller with Eintracht Frankfurt in 1993-94.
They have also won each of their last five top-flight games without conceding a goal, something they last achieved under Carlo Ancelotti between February and April 2017.
They last recorded a longer run of top-flight wins coupled with clean sheets between November and December 2014 under Guardiola (six).
"The last results are gone now. I just want us to win the game tomorrow. It's the Klassiker," Kompany told a press conference on Friday.
"I like that these games have this special build-up. We all look forward to these games."
"If you look at the big picture, it's important for us not to look too much at how others see our players. It's how we see them that's important."
Bayern make the trip to the Westfalenstadion on Saturday, taking on a Dortmund side who have failed to replicate their Champions League displays in the Bundesliga.
Not helped with several injuries within their ranks, Nuri Sahin's side sit fifth in the table, 10 points behind Bayern ahead of their 136th top-flight meeting.
And despite failing to win any of their five away games in the Bundesliga so far, Dortmund have impressed on home soil.
They are the only side to have won all of their home games in the Bundesliga this season (six), with PSG and Barcelona the only other teams in Europe's top five leagues yet to drop a point at home.
Sahin is also the first Dortmund coach since the Bundesliga was founded to win each of his first eight competitive home games in charge.
BVB could now start a campaign with nine straight home wins in all competitions for the first time in professional football. Including last season, Dortmund have won each of their last 11 home matches – they have only ever enjoyed a longer run in 1994 under Ottmar Hitzfeld (14).
And Kompany is expecting a difficult test for his side, saying: "Our preparation is for the best version of the team.
"If they are top then they go high into their pressing game, they are extremely dangerous on the break with their speed on the wings.
"When they are at their best, they are also very, very good at building up the play. It's not going to be an easy game, it'll be tough."
Neuer missed the Bundesliga win over Heidenheim on Saturday and joins a number of Bayern players on the injury list.
The 38-year-old was hurt in the German Cup loss to Bayer Leverkusen last week after crashing into an opponent and getting sent off with a straight red card, his first ever.
"He is nursing a broken rib. He will most likely not play any more this year. It is important for this to heal and from January we'll have him again," Kompany told reporters on Monday.
"It's not too bad, but with so many matches it's too early for him to play."
Bayern are already without injured top scorer Harry Kane, Joao Palhinha, Alphonso Davies and Serge Gnabry among others for Tuesday's game with Shakhtar Donetsk.
But with the winter break approaching, Kompany said the Bundesliga leaders have done well so far to compensate for the absences.
The Bavarians are in 13th place on nine points in the Champions League table and are a point outside the top eight, who automatically qualify for the last 16.
Hosts Shakhtar, who will stage the game in Gelsenkirchen, are 26th on four points, two points off the playoff places.
"The issue of injuries is that clearly we have a lot of people absent but we held on well until now," Kompany added.
"From early January we will have a big squad again. We handled it well so far."
Nathan Tella's second-half strike proved the difference as Xabi Alonso's side booked their place in the quarter-finals.
The hosts were reduced to 10 men after just 17 minutes, when Manuel Neuer received the first red card of his career after bringing down Jeremie Frimpong just outside the box.
Despite the numerical disadvantage, Vincent Kompany's side created the better chances during the first half, with Kingsley Coman, Konrad Laimer and Leon Goretzka going close.
However, the visitors broke through against the run of play in the 69th minute, when Tella nodded in from Alex Grimaldo's cross.
Michael Olise almost snatched a dramatic equaliser with a curling effort in stoppage time, but Leverkusen survived to maintain their title defence.
Data Debrief: Nine in a row for Leverkusen and Alonso
Bayern had won each of their five previous DFB Pokal matches against the defending champions.
However, that streak ended here as they have now suffered successive eliminations after home defeats (also losing to Freiburg in April 2023) for the first time in their history.
As for Leverkusen, they have now won their last nine DFB Pokal matches and kept clean sheets in their last five - both their longest such streaks in the competition since at least 2005-06.
Meanwhile, Alonso has won all nine of his DFB Pokal matches as a coach. Only two coaches have enjoyed longer undefeated starts in the competition this millennium - Louis van Gaal and Pep Guardiola (both in the first 10).
Germany international Musiala scored with a bullet header from close range in the 67th minute with Bayern dominating and missing several chances before eventually breaking the deadlock.
Musiala’s chance was set up when Harry Kane headed Leroy Sane’s cross back across the face of goal.
The result was much needed to get Bayern’s campaign back on track, with the win seeing them bounce back from suffering two consecutive defeats in the competition – against Aston Villa and Barcelona – for the first time since 2017.
A win lifted the Germans to six points from four matches and into 17th place with Benfica, who were toothless in attack, also on six points in 19th place.
Europe's top club competition has switched from a group stage to a league phase this season, where 36 teams play eight matches each. The top eight in the table progress directly to the next round, while the next 16 teams enter a two-legged playoff.
Bayern have a crunch clash against Paris Saint-Germain next in the competition on November 26.
Data Debrief: Unlucky 13 for Benfica
Benfica have now played 13 major European matches against Bayern and have never tasted victory, collecting only three draws and suffering 10 defeats.
That trend rarely showed signs of ending in this match, with Benfica not threatening. The visitors failed to register a shot on target for the first time in 45 Champions League matches. The last time they did not trouble the goalkeeper in this competition was in October 2017 against Manchester United. Bayern, by comparison, racked up 10 attempts on target.
Benfica also only had four touches in the opposition box, their lowest tally on record since Opta started recording that data in the Champions League in 2007-08, with Bayern tallying 51.
As for Kane, the assist means he has now been directly involved in 80 goals across all competitions (61 goals, 19 assists) since the start of last season. That is 16 more than any other player across Europe’s biggest five leagues in this period.
Kim Min-jae's first-half header proved decisive at Allianz Arena on Tuesday, with Ousmane Dembele's red card after the break making the task even tougher for PSG.
Having won just once in the competition so far – back in their opening game against Girona – Luis Enrique's team were second-best for much of the contest.
Bayern dominated the first half, with Kingsley Coman particularly dangerous, and the Bundesliga leaders got the goal their performance merited when Kim headed home from a corner in the 38th minute, with PSG's stand-in goalkeeper Matvey Safonov in no man's land.
Dembele, who had seen a decent attempt saved by Manuel Neuer in the first half, received his marching orders for a lunge on his France team-mate Coman just before the hour, with the referee deeming it worthy of a second booking. It marked the first time Dembele has been sent off since 2019, when he saw red for Barcelona in a LaLiga clash with Sevilla.
Safonov made amends for his earlier mistake by tipping a Jamal Musiala shot onto the post but despite applying some late pressure, PSG could not prevent Bayern from claiming a seventh consecutive victory and seventh straight clean sheet in all competitions.
While Vincent Kompany's team are up to 11th in the standings, PSG are in 26th on just four points from their five matches, two places outside of the play-off spots with three games remaining.
Data Debrief: Kim off the mark for buoyant Bayern
Kim scored his first goal in the Champions League, in what was his 23rd appearance in the competition.
The scoreline ultimately flattered PSG, who finished with 0.88 expected goals (xG), while Bayern created 2.21 xG.
Bayern are now unbeaten in each of their last 33 home games in the Champions League group stage (W31 D2), the joint-longest such run in the competition's history, level with Barcelona between November 2009 and November 2020. They have gone on a run of seven wins without conceding for the first time since September 2011, too.
This is the eighth time in the Champions League that Bayern have defeated PSG, with only Real Madrid (11 vs Bayern) and Bayern themselves (10 vs Barcelona) winning more games against a single opponent in the competition's history.
Two long-range strikes, one from Robert Andrich and another from Aleksandar Pavlovic, ensured a share of the spoils on Saturday.
Defending champions Leverkusen scored with their first chance in the 31st minute when Granit Xhaka controlled a corner with his chest and set up Andrich outside the box, with the Germany international's sweeping low shot drilled through a crowd of players into the bottom corner.
Their lead did not last long, however, as a poor clearance fell to Pavlovic and the midfielder pulled the trigger from 25 yards with a half-volley that brushed the fingertips of goalkeeper Lukas Hradecky as it sailed into the top corner.
With Serge Gnabry having hit the post and then crossbar in quick succession, Bayern dominated proceedings in the second half, with Leverkusen pegged back. The hosts boasted an expected goals (xG) total of 1.32 at full-time compared to their opponent's meagre 0.07xG.
But despite their 18 shots, Bayern could not clinch a decisive second goal.
Bayern stay top with 13 points, while Xabi Alonso's Leverkusen are third with 10 points, a point behind RB Leipzig, who thrashed Augsburg 4-0.
Data Debrief: Wonderstrikes and fine margins
Bayern hit the woodwork twice through Gnabry in a matter of seconds, but ultimately only managed to get three attempts on target, while Pavlovic's stunning equaliser came with an xG value of just 0.02.
That being said, Leverkusen - who hammered Bayern 3-0 in their last meeting - hardly offered much going the other way, having just three attempts in total.
This top-of-the-table clash also marked the first time in three years that Harry Kane has not attempted a single shot after starting a league match. The last time was when he represented Tottenham against Crystal Palace in September 2021.
Their one goal, however, does mean Bayern have scored in their last 12 games in the Bundesliga, scoring 33 goals in that run.
Maximilian Eggestein's well-worked goal gave the visitors a deserved lead late in the first half before the champions struck back through Kingsley Coman after the hour.
But they were unable to build on their equaliser as a dogged performance from Florian Kohfeldt's men earned a deserved share of the spoils.
Werder travelled to the Allianz Arena having avoided defeat in their previous four outings, though each of those ended in draws.
And, with Bayern having earned 10 consecutive victories coming into this fixture, they would've expected to dominate from the off, rather than give up the best of the first-half chances.
However, only a brilliant Manuel Neuer save denied Josh Sargent from close range early on, before Leonardo Bittencourt volleyed into the side-netting when he might have done better.
The hosts' rhythm was no doubt damaged by the early loss of Theo Hernandez to injury, a blow that saw Leon Goretzka introduced and both Javi Martinez and David Alaba change position.
Werder capitalised on that uncertainty at the back as Sargent burst in behind down the flank being marshalled by Martinez and Alaba, before pulling back for Eggestein to sidefoot home just before half-time.
Milot Rashica should've made it two shortly after the restart, taking too long in a one-on-one situation, prompting Douglas Costa to respond by cracking the bar with a deflected effort.
That marked the start of a spell of long overdue Bayern pressure that finally told when Coman headed in Goretzka's right-wing cross at the back post.
But, despite the introduction of Leroy Sane and Serge Gnabry off the bench, Hansi Flick's men struggled to create much of note in the final half-hour.
In fact, only another fine one-handed stop from Neuer prevented the visitors from snatching the win through Sargent with five minutes of normal time remaining.
After a lacklustre first half at the Allianz Arena, midfielder Muller provided the game's decisive moment early in the second period with a beautifully controlled finish.
Augsburg had two late chances as Florian Niederlechner saw a close-range effort saved by Manuel Neuer before he put in the ball net shortly after only to see it chalked off for offside.
Bayern sealed the points in injury time when Leon Goretzka slipped the ball home after a neat interchange of passes with Serge Gnabry.
Harry Kane was also on target from the penalty spot for the hosts, who made it two Bundesliga wins from two under Vincent Kompany.
Bayern broke through in the 38th minute after Max Rosenfelder was penalised for handball following a VAR review.
Kane stepped up and made no mistake as he calmly sent Freiburg goalkeeper Florian Muller the wrong way from 12 yards.
Thomas Muller climbed off the bench to seal the victory 12 minutes from time, controlling Serge Gnabry's cross before firing into the roof of the net.
Freiburg had the opportunity to grab a consolation in stoppage time after Joao Palhinha handled Ritsu Doan's shot, but Lucas Holer blazed over from the penalty spot.
Data Debrief: Muller marks historic day with landmark goal
The day belonged to Muller, who surpassed Sepp Maier to become Bayern's record appearance maker outright with 710. Fittingly, he marked the occasion with his 150th Bundesliga goal.
The 34-year-old has not found the net in a joint-record 16 successive German top-flight seasons, matching Holger Fach, Mats Hummels, Bernd Nickel, Olaf Thon and Michael Zorc.
Earlier on, Kane maintained his perfect record from the penalty spot in Bundesliga with six consecutive successful kicks.
The England captain has scored against all 17 opponents he has faced in Bundesliga, with only Miroslav Klose facing more opponents and netting against all of them (28).
Hansi Flick's treble-winning outfit struggled against a stubborn Sevilla side who had been unbeaten since February – a run that included a record sixth triumph in the Europa League, formerly the UEFA Cup – and the LaLiga side went ahead through Lucas Ocampos' penalty.
Leon Goretzka levelled before half-time but Bayern's run of 22 successive victories would have come to an end had Youssef En-Nesyri not been thwarted by Manuel Neuer in the dying stages of normal time.
But it was fellow substitute Martinez, linked with a return to Athletic Bilbao after eight years in Bavaria, who scored his first goal since April 2019 to earn Bayern yet more silverware.
Bayern opened their 2020-21 season with an 8-0 rout of Schalke but it was Sevilla who struck first through Ocampos' penalty.
Luuk de Jong's cushioned header reached Ivan Rakitic, and the midfielder – back at the club after re-joining from Barcelona – was barged over by David Alaba, with Ocampos outfoxing Neuer from a no-look spot-kick.
Robert Lewandowski failed to beat Yassine Bounou from a one-on-one as Bayern responded, but he made up for that before half-time, laying the ball back for Goretzka to pick his spot and score the equaliser.
The Champions League winners thought they had the lead within six minutes of the restart after Muller teed up Lewandowski, having initially been presented with the chance himself by the Pole, but VAR spotted Bayern's number nine was offside when first collecting Leroy Sane's pass.
It was one-way traffic thereafter as Bounou denied Serge Gnabry and Diego Carlos blocked the rebound from Sane, who had a goal disallowed himself after Lewandowski was adjudged to have fouled Sergio Escudero in the build-up.
But it was Sevilla who should have won the game in normal time when Jesus Navas released En-Nesyri on a counter-attack, only for Neuer to make the save from an attempt that was too easy to anticipate.
Sevilla had renewed optimism at the start of the additional period, though En-Nesyri looked offside when he aimed an effort at goal that Neuer's right foot diverted onto a post.
And Martinez made him pay five minutes after coming on when he directed a header past Bounou after the goalkeeper could only push Alaba's effort back in front of him.
Kane opened the scoring in the 63rd with a penalty before netting a quickfire double in second-half stoppage time to smash the record previously held by Erling Haaland.
Despite controlling the early possession, Bayern were unable to make their dominance count, with Nediljko Labrovic rarely troubled in the opening 45 minutes.
The hosts maintained their dominance after the interval, with Leon Goretzka's looped header grazing the crossbar before Jamal Musiala went close soon after.
However, Bayern were awarded a penalty after a lengthy VAR review saw Mads Pedersen penalised for handling the ball, with Kane stepping up to score from 12 yards.
The England captain grabbed his second of the game in the third-minute of stoppage time following another VAR review which saw Keven Schlotterbeck sent off after tripping Kane inside the box.
Kane sent Labrovic the wrong way but was not to be denied a fourth treble of the season, brilliantly taking down Goretzka's searching ball before heading the ball home.
Data Debrief: HurriKane
Kane has now scored 50 Bundesliga goals in 43 matches. Before him, Haaland was the quickest player to reach 50 Bundesliga goals, having done so in 50 appearances in the competition for Borussia Dortmund.
He is also the quickest to reach that total for Bayern by some distance. Kane has reached that tally quicker than the likes of Gerd Muller (83 games), Mario Gomez (71 games), Roy Makaay (67 games) and Robert Lewandowski (64 games).
10 of Kane’s goals have come from penalties, while 32 of them have been with his right foot, nine with his left and nine with his head.
Vincent Kompany's team moved, temporarily at least, to the top of the Bundesliga standings with the minimum of fuss at the Allianz Arena.
The Bavarians, who host Benfica in the Champions League on Wednesday, opened the scoring with a 15th-minute penalty from England captain Kane before Kingsley Coman curled a shot past keeper Frederik Ronnow to make it 2-0 two minutes before the break.
Union were constantly on the back foot and could do nothing to stop Kane from stabbing in his second goal from close range six minutes after the restart.
Kane, who also scored a hat-trick against Stuttgart two weeks ago, now has 11 league goals this season.
Undefeated in the league and eager to reclaim domestic dominance after last season's double by Bayer Leverkusen, Bayern have now scored 32 goals and conceded seven in nine Bundesliga games.
Data Debrief: Goals, goals, goals
Bayern just cannot stop scoring. While they may be struggling in the Champions League, they are flying domestically, and they have now netted 50 times under Kompany in all competitions this season.
They are the first club from Europe's five major leagues to reach the 50-goal mark in this competitive season.
Meanwhile, since detailed data collection in 2004-05, only one player has collected more direct goal contributions in the first nine matchdays of a Bundesliga season than Kane this season (16), and that was the former Tottenham captain himself last year.
Bayern gave starts to goalkeeper Sven Ulreich, resting Manuel Neuer, and wingers Michael Cuisance and Sarpreet Singh after clinching the title with victory at Werder Bremen on Tuesday.
Hansi Flick's men were still dominant at the Allianz Arena with Lewandowski - whose goal at the Weserstadion wrapped up an eighth successive Bundesliga crown - unsurprisingly to the fore.
Lewandowski teed up Joshua Kimmich for the opener and his brace, separated by a response from Lucas Holer, secured a routine win that ends Freiburg's Europa League hopes.
His double takes Lewandowski to 33 Bundesliga goals this term, meaning he has sole ownership of the record for most goals in a season by a non-German player.
Despite their changes, Bayern were on the front foot from the off and after 15 minutes they got the reward their start deserved.
Talisman Lewandowski turned provider as he laid the ball off on the edge of the area, Kimmich making no mistake as he slotted into the bottom-left corner.
Lewandowski was soon celebrating his 32nd league goal of the season, though, the Poland international given the simplest of tasks as he nodded in on the rebound after Alexander Schwolow could only parry Leon Goretzka's low effort into the air.
Freiburg halved the deficit against the run of play as Jonathan Schmid's shot from a tight angle deflected off Ulreich and into the path of Holer to tap in from point-blank range.
However, the two-goal cushion was swiftly re-established as Bayern took advantage of some haphazard defending from the visitors.
Lucas Hernandez was left in far too much space on the left flank and his low near-post cross was deftly turned home by Lewandowski.
Only a superb diving save from Schwolow denied Thomas Muller a goal on his 350th Bundesliga appearance after Freiburg sloppily conceded possession on the edge of their own box.
Bayern took their foot off the gas in the second half but easily saw out the game and were denied a late fourth by the woodwork as substitute Kingsley Coman struck the crossbar.
What does it mean? - Brilliant Bayern end Freiburg dream
On the hunt for the treble, Bayern look well set to challenge for Champions League glory in Lisbon next month. Freiburg's dreams of continental competition next season are over because of this result and wins for Wolfsburg and Hoffenheim.
Lewandowski surpasses Aubameyang
It would take something incredible for Lewandowski to break Gerd Muller's record of 40 goals in a single Bundesliga season next weekend but, after tying Pierre-Emerick Aubameyang's record of 31 from 2016-17, he surpassed the former Borussia Dortmund striker with a typically clinical display of finishing.
Freiburg falter at the back
Defensive solidity was required for Freiburg to have a hope of claiming a shock result. They offered anything but, much to the annoyance of coach Christian Streich on the touchline.
What's next?
Bayern round off a unique but ultimately triumphant league campaign at Wolfsburg on Saturday. Freiburg bid farewell to the Schwarzwald-Stadion, with Schalke the final visitors before they move into a new stadium next season.
The midfield general in the mighty Bayern machine won the ball in the centre circle and bundled in after exchanging passes with Robert Lewandowski for the 82nd-minute clincher.
Corentin Tolisso and Thomas Muller had earlier put Bayern 2-0 in front, but Julian Brandt and Erling Haaland brought Dortmund back to level terms.
Victory meant Bayern, whose 32-game unbeaten run ended with defeat at the weekend to Hoffenheim, delivered more success in the Hansi Flick era.
Kane, who had missed a golden chance in front of goal in the 51st minute, broke the deadlock six minutes later, rifling in from outside the box.
The England captain, who had not scored in his previous two Bundesliga games, then drilled in following a goalmouth scramble on the hour.
He secured his hat-trick in the 80th minute with his eighth league goal of the season after Joao Palhinha's shot was blocked, with substitute Kingsley Coman curling in Bayern's fourth goal in the 89th.
The result keeps the Bavarians at the top of the standings on 17 points, with a better goal difference than RB Leipzig, who were 2-0 victors at Mainz earlier on Saturday.
Freiburg are third on 15 with champions Bayer Leverkusen in fourth, one point back after their 2-1 win over Eintracht Frankfurt.
Data Debrief: Goals galore for Kane and Bayern
This marked Kane's third hat-trick of the season for Bayern in all competitions. It brings his tally in the Bundesliga to eight goals this season, topping the charts at Bayern.
Bayern have scored in their last 14 games in the Bundesliga, their longest run of games with a goal in the competition since a run of 43 games from September 30, 2022 to January 12, 2024.
Bayern are also unbeaten in their seven games so far this season and have scored at least six more goals than any other team in the division (24, Leverkusen have 18).
