Mohamed Salah's late goal gave Liverpool the lead before Darwin Nunez's stoppage-time sealer secured a 2-0 win over Napoli to give Jurgen Klopp victory in his 400th game in charge, ending the visitors' unbeaten start to the campaign.
Both sides were already assured of a place in the knockout stages of the competition, with only a four-goal winning margin enough to see Liverpool usurp Napoli in top spot.
The Reds managed two late strikes courtesy of Salah and Nunez, with Salah scrambling one over the line in the 85th minute after Alex Meret just about kept out substitute Nunez's header.
Nunez added a second from the final act of the match as Napoli, who earlier had a Leo Skiri Ostigard effort ruled out for offside, saw their unbeaten run ended at 17 matches.
Neither team could really find any rhythm in a quiet first half that took half an hour for the first shot on target to arrive, with Tanguy Ndombele forcing a save out of Alisson.
Liverpool attacked up the other end and only an Meret stop prevented Thiago Alcantara from opening the scoring, shortly before Curtis Jones headed just over the crossbar.
Ostigard guided Khvicha Kvaratskhelia's free-kick delivery past Alisson eight minutes into the second period, but VAR – after a three-minute wait – ruled the defender was offside.
Kvaratskhelia then had a powerful volley saved by Alisson as Napoli, who had won their previous five group outings with a competition-high 20 goals, pushed for a winner.
A winner did arrive, albeit at the other end as Meret prevented Nunez's header from crossing the line, but Salah was there on the follow-up to poke over the line.
Nunez, introduced in the 73rd minute, added further gloss to the scoreline when tapping in a saved Virgil van Dijk header from under the bar.
What does it mean? Victory for Klopp on milestone occasion
Liverpool did not win by the four-goal margin required, which was never likely against in-form Napoli, meaning they will be unseeded in Monday's draw for the last 16.
But the Reds at least manage to put Saturday's league loss to Leeds United behind them with a narrow, if arguably slightly undeserved, victory in Klopp's 400th match in charge.
It was also the German's 100th Champions League game in his career, making him the seventh manager to reach that figure.
Darwin's chaotic cameo
Nunez has gained a reputation of being an 'agent of chaos' because of his erratic playing style, and so that proved in his 20 minutes or so on the field against Napoli.
He played a big part in the opening goal and then added a late second, albeit after a nervy VAR check, for what was his first Liverpool goal in the Champions League.
Spalletti's side thwarted
Napoli had won 13 games in a row entering this match, including five from five in the Champions League with 20 goals scored – four short of Bayern Munich's all-time record.
The Serie A leaders managed just two shots on target and accumulated an expected goals (xG) value of 0.43, with this going down as an off-day for Luciano Spalletti's talented side.
What's next?
Liverpool will look to reignite their Premier League campaign when they travel to Tottenham on Sunday, while Serie A leaders Napoli head to second-place Atalanta on Saturday.
Sheffield United go second after late turnaround, Plymouth continue good home form
Sheffield United staged a late turnaround to win 2-1 away to Bristol City and go second in the Championship, one point behind leaders Sunderland who play on Wednesday.
The game started slowly, with the hosts not opening the scoring until a 75th-minute Anis Mehmeti penalty after a foul on Sinclair Armstrong by goalkeeper Michael Cooper.
The Blades showed great character to haul themselves back into the game, with 18-year-old Ryan One scoring the equaliser in the 86th minute.
But things went up a notch in stoppage time when Robert Dickie was given a straight red card for a cynical foul on Callum O'Hare 35 yards out.
The drama wasn't finished yet and with seconds to go, Harrison Burrows smashed home a left-foot rocket to win the game for the Blades.
At the bottom of the table, Plymouth opened a four-point gap between themselves and the relegation zone with a 1-0 victory over bottom-of-the-table Portsmouth.
The victory means that Wayne Rooney's side have dropped just two points in their last five games at Home Park, having lost six on the bounce in all competitions away.
It is now four without a victory for Portsmouth, who have earned just nine points in their opening 14 matches back in the Championship.
Elsewhere, Middlesbrough responded to their 3-0 defeat at home to Coventry City last weekend by beating second-bottom Queens Park Rangers 4-1 on the road.
That was a first victory in three for Michael Carrick's side, who are one place below the play-off positions and trail only by goal difference.
QPR are four points behind fourth-bottom Preston North End, having failed to win any of their last 10 league games.
Liverpool 4-0 Leverkusen: Diaz nets second-half hat-trick to extend 100% start
Luis Diaz scored a second-half hat-trick for Liverpool in their 4-0 victory at home to Bayer Leverkusen as they maintained their 100% start to their Champions League campaign.
Arne Slot's side lead the 36-team league within Europe's main competition following the result, with only Aston Villa alongside them as the only other club to have won every game. They play Club Brugge on Wednesday in their fourth match.
Back in Liverpool, things got off to a slow start with the scores level until the 61st minute. Diaz lifted the ball over goalkeeper Lukas Hradecky to get things moving before Cody Gakpo made it two just two minutes later.
Gakpo's goal was initially ruled offside by the on-field official, though was overturned following a VAR review.
Diaz then scored his second and Liverpool's third of the night in the 83rd minute after picking up Mohamed Salah's cross and slotting past Hradecky. The Colombian rounded things off deep into stoppage time with a tap in from close range.
The result leaves Leverkusen 11th in the table with seven points, having tasted their first defeat of the competition at Anfield.
Data debrief: Slot has Liverpool purring
Liverpool are now top of both the Champions League standings and the Premier League and continue to go from strength to strength under Slot.
They looked much more threatening in the second half compared to the first, registering 3.48 xG in the second period after just 0.64 in the first half.
Diaz, meanwhile, has now scored nine goals in 15 matches in all competitions.
Al-Nassr 5-1 Al-Ain: Ronaldo on target in AFC Champions League win
Cristiano Ronaldo powered Al-Nassr to a convincing 5-1 triumph over Asian Champions League Elite holders Al-Ain on Tuesday.
The victory carried a sense of redemption for Al-Nassr as they avenged last season's semi-final defeat to the same opposition on their way to lifting a second title in the competition.
Talisca fired the hosts into a fifth minute lead with a well-taken effort from the edge of the box before Ronaldo poked home his 908th career goal just after the half-hour mark.
Visiting defender Fabio Cardoso then deflected Angelo's effort beyond Khalid Eisa to hand Al-Nassr a comfortable advantage at the interval.
Al-Ain did, however, pull one back early in the second half when Park Yong-woo's strike struck the post and went in off the back of Al-Nassr goalkeeper Bento.
But the result was put beyond doubt late on when Wesley curled home Al-Nassr's fourth, before Talisca notched his brace in second half stoppage time.
Data Debrief: Return of Ronaldo
After winning five Champions League across his glittering career, Ronaldo is now eyeing a first AFC Champions League crown with Al-Nassr.
The 39-year-old has six goals in eight appearances in the competition, with his goal against Al-Ain ending a three-game goal drought for Al-Nassr.
Ronaldo also registered a team-high expected goals (xG) tally of 1.25 towards Al-Nassr's 2.67 total, while also producing more shots (eight) and touches in the opposition box (nine) than any other player on the pitch.
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