A second-half penalty from Khvicha Kvaratskhelia earned them a 1-0 win, but they could easily have been trailing at the break due to a sluggish start.
They were outplayed in the first half by Empoli, who had 10 shots, four of which were on target, and accumulated 0.66 expected goals (xG), compared to the visitors, who only managed three efforts without testing Devis Vasquez.
Napoli finished the match with just one shot on target, the goal, and Conte recalled their dismal title defence last season along with their 3-0 opening-day defeat to Verona to highlight how their approach has changed when they struggle to break down stubborn opponents.
"In the first half we were spectators, I didn't see what we had prepared, and I saw a lot of nervousness," Conte told reporters.
"Certainly, what satisfies me is to have seen a reaction in the second half. The first was very negative.
"This is a difficult place to come. I don't know if it was due to the fact of defending the top spot, but it makes me smile if I think about last year or how we started this season."
The penalty is the first goal that Empoli have conceded at home this season, as the hosts suffered their second consecutive defeat.
Conte sent on Giovanni Simeone for Romelu Lukaku and replaced Leonardo Spinazzola with Mathias Olivera just before the hour mark to try and inject something different into the game.
Seconds later, they were awarded the decisive penalty, and Conte was pleased that the changes paid off.
"When you work during the week you prepare the game in all phases, we had prepared it defensively with 4-5-1," Conte added.
"I changed something from a tactical point of view, from a possession point of view. I think it bore fruit because we saw another game."
After narrowly edging past Serie B side Modena on penalties in the Coppa Italia first round in his first game, Conte followed it up with a 3-0 defeat to Verona in his first league match.
Since then, Napoli are unbeaten, winning six of their next seven games, only dropping points in a goalless draw with the Italian's former club, Juventus.
However, despite their impressive form, Conte is wary of getting too carried away.
"We are with the 'work in progress' sign, it cannot be otherwise after only three months," Conte told a press conference ahead of Sunday's game at Empoli.
"Otherwise, we would all underestimate the path that needs to be taken in a reconstruction phase like ours. We're just getting started.
"Victories are built, they are not invented, but what I feel I can guarantee is to rebuild solid foundations that can last over time."
The international break has left Conte without midfielder Stanislav Lobotka, injured while playing with Slovakia.
Lobotka has started all seven league games under Conte and was an ever-present in the starting side last season, but the manager is confident that Scotland international Billy Gilmour is ready for what will be his first Serie A start.
"It's not a very serious problem but we have to face it and recover, obviously I'm sorry because he was expressing himself at very high levels, but at the same time it will be an opportunity to see Gilmour," Conte said.
"Billy knows what he has to do, he hasn't trained only in these two days, but from the beginning. It changes little, the characteristics are very similar. If Gilmour hadn't been there it would have been different."
Napoli's bid to remain on top will face a stern test away to Empoli. The Tuscan side have lost only once this season, and have the second-best defensive record in Serie A, conceding four goals in their seven games.
"We are talking about a team that suffered their only defeat before the break, in the last minutes and on a difficult pitch, against Lazio at the Olimpico," Conte said.
"It is precisely in these matches that the spirit of sacrifice, according to the Empoli players, becomes an important weapon for them.
"I will not tolerate a spirit of sacrifice inferior to that of Empoli."
Kvaratskhelia tucked away his spot-kick in the 63rd minute, Napoli's only shot on target over the 90 minutes and the first goal Empoli have conceded at home in the league this season.
Tino Anjorin was the player to concede the penalty, standing on Matteo Politano's foot inside the area on the Napoli winger's 300th Serie A appearance.
Empoli were left to rue missed chances in the first half when they were by far the better side, with Sebastiano Esposito going closest when his ferocious volley was kept out by Elia Caprile.
Caprile was also called upon to stop Giuseppe Pezzella's effort with his foot as Antonio Conte's men earned a scrappy win, their fourth in a row in all competitions.
Napoli moved on to 19 points, three ahead of Juventus in second with Inter third on 14 before they face Roma later on Sunday. Empoli are 11th with 10 points.
Data Debrief: Kvara on the spot
Kvaratskhelia has scored four league goals this season, a tally only bettered by four players in Serie A – Marcus Thuram, Mateo Retegui (both seven), Christian Pulisic and Dusan Vlahovic (both five).
The Georgian has now scored three penalties in the competition overall, with each of those coming in away games.
Inter's victory at Stadio Carlo Castellani sees them close the gap on Serie A leaders Napoli to four points.
Empoli faced an uphill battle when Saba Goglichidze was shown a red card for a studs-up high challenge on Marcus Thuram after half an hour, and Inter made the extra man count in the second half.
Frattesi found the net five minutes after the break and doubled Inter's lead in the 67th minute, before Martinez rounded off the win 11 minutes from time, stretching Empoli's winless run to five games.
Inter, now unbeaten in five league games, remain second in the standings with 21 points, behind Napoli on 25 after their 2-0 win at AC Milan on Tuesday. Empoli remain 11th on 11 points.
Data Debrief: Inter register another Empoli shutout
Inter have now kept a clean sheet in their past 10 away games against Empoli in Serie A, extending the record for one club against another in the competition's history.
Frattesi was the star performer for the visitors with his double, making him the highest-scoring Italian midfielder across Europe's top five leagues for club and country this season with six goals to his name.
Inter did well to keep out Empoli, who have failed to score in 10 of their past 15 home games in Serie A - the worst return of any side in the league.
Inter booked their place in the Champions League semi-finals in midweek, but their poor domestic form – coupled with Juventus' points reprieve – had seen them drop to sixth.
Simone Inzaghi's heavily rotated side took time to get going against Empoli, but Lukaku gave them a 48th-minute lead with his first league goal from open play since August.
Lukaku fired in another in the 76th minute and then teed up substitute Lautaro Martinez late on to seal the points that lift Inter up to fifth – temporarily at least – and within two points of fourth-placed Roma, who face Atalanta on Monday.
Samir Handanovic was one of those recalled between Inter's two cup ties and was equal to efforts from Nicolo Cambiaghi and Tommaso Baldanzi in the opening 20 minutes.
Roberto Gagliardini fired over from range as Inter struggled to create anything of note in a low-key first half, but Inter got their breakthrough three minutes into the second period.
Through his first sight of goal, Lukaku guided a precise shot away from Samuele Perisan into the bottom-left corner for just his fourth league strike of the campaign.
Empoli, now with just one win in 12 league games, offered little in response and fell further behind when Lukaku worked a yard of space and fired an angled shot past Perisan.
Lukaku was not finished there as he carried the ball forward and played in Martinez to convert from one-on-one and complete the routine victory.
Danilo D'Ambrosio headed in the opener for Inter after 33 minutes but Empoli felt Nedim Bajrami had been fouled at the other end by the Nerazzurri centre-back.
Federico Dimarco subsequently added a second following Samuele Ricci's dismissal for a reckless challenge on Nicolo Barella, leaving Andreazzoli fuming over the standard of officiating in Wednesday's Serie A clash.
"I want to be very clear that I have never talked about referees, because I think they ought to be defended as a profession," Andreazzoli told Sky Sport Italia.
"However, I want to know what exactly Paolo Valeri was doing this evening at the VAR desk. Either he was distracted or he popped to the bathroom or something, because how is it possible that VAR does not help the referee when it has to?
"Let’s leave aside the Inter performance, just like the red card for Ricci, which I’ll admit was basically an orange card and I accept that. I always accept decisions.
"However, if VAR sees a clear and obvious error, I ask myself why do they not help the referee? That is what they are there for.
"Honestly, even my four-year-old grandson Tommaso could see that was a penalty. I saw it on a phone when I went back into the locker room at the final whistle and was shocked when I saw the replay.
"If we do not use these instruments and this technology, then we remove the objectivity of refereeing in games. The matches must be objective. The referee did a good job overall, but he didn’t see that incident, the VAR did, so help him make the right decisions."
Inter managed a seventh consecutive top-flight clean sheet on the road against Andreazzoli's team – their best run against a single opponent in the competition and tied for the best streak of any one side against another.
At the other end, Alexis Sanchez assisted D'Ambrosio's opener - his 21st goal involvement in 23 Serie A starts with the Nerazzurri in Serie A (nine goals, 12 assists) - and Inter's assistant manager Massimiliano Farris was quick to praise the Chile international.
"It’s true that his characteristics are fairly unique within the team, but Joaquin Correa could do something similar if called upon," Farris said post-match to Sky Sport Italia.
"Alexis has that creativity, that moment of magic, you just need to see the assist for D’Ambrosio’s goal.
"D’Ambrosio and Dimarco are added value to this squad and bring more than you’d expect.
"It’s a pity Lautaro Martinez didn’t score today, but he’s saving his goals for other games. We made a few changes, everyone showed they were ready when called upon, as everyone has to work together as a team."
Inter remained 13 points behind runaway leaders Napoli after going down 1-0 at home following a first-half Milan Skriniar red card.
Empoli were good value for their win against Inzaghi's out-of-sorts side, and the head coach appeared to recognise that as he sought to move on swiftly from this match.
"We have to archive it immediately," he said. "We will have another difficult game, and we have to forget immediately, looking ahead.
"Of course, we will analyse the mistakes, but we have to think about the next matches."
The season is now at the halfway stage, and Inzaghi acknowledged Inter must improve.
"This is a defeat that stings," he told DAZN. "We finish the first half of the season with 37 points and many regrets.
"Now, we know we'll have to do better over the second part."
However, midfielder Hakan Calhanoglu is remaining optimistic, saying in an interview with Sky Sport: "Thirteen points [to Napoli] is a huge gap, but we have to keep going and not stop.
"I know it feels hard to believe, but there's still a long way to go."
Kean had not scored since April, but the striker set Juve on their way to victory with an early strike at the Allianz Stadium.
Weston McKennie doubled the Bianconeri's lead with his first Serie A goal of the season, heading home in the second half, and Rabiot added a late double to cap an impressive performance.
That is now back-to-back wins for Massimiliano Allegri's side, who moved up a place to seventh ahead of a must-win Champions League clash at Benfica next week.
Juve started with great intensity and were rewarded just eight minutes in when Filip Kostic whipped in a cross from the left and an unmarked Kean applied the finish from close range.
Kean should have found the net again just after the half-hour mark but headed a McKennie cross wide from six yards out.
The Bianconeri demonstrated the danger they pose from set-pieces to double their lead nine minutes into the second half, McKennie rising to powerfully head Juan Cuadrado's delivery into the roof of the net.
Kean nodded in another sublime Kostic delivery but had his celebrations cut short after straying offside as hungry Juve continued to cause problems.
Juve scored another goal from a Cuadrado corner after 82 minutes, Guglielmo Vicario unable to palm away Rabiot's header before it crossed the line.
The France midfielder then capped a great evening for the Turin giants when Danilo's cross gave him a tap-in at the end.
Motta has made a strong start at Juve since joining from Bologna, with an unbeaten start to the Serie A campaign putting them level with Scudetto holders Inter at the summit.
Next week, the Bianconeri face PSV in their first Champions League game since 2022 before welcoming Napoli to Turin for a huge clash on September 21, but Motta will not look beyond Saturday's visit to the Stadio Carlo Castellani.
"The other two games of the week we have time to think and prepare for. The focus is tomorrow. Then we will think about the other games," Motta said on Friday.
"We only have to think about the game against Empoli.
"Tomorrow will be a complicated match like all the games you face in Serie A, against a team that is doing well that knows what they want to do on the pitch."
Empoli are also unbeaten after three league games, sitting just two points behind Juventus in seventh place, and Motta won't be taking the Tuscan side lightly.
"We face an Empoli team that is doing well right now, they have played three really good games, but we are also in good shape," Motta said.
"We knew the calendar and the games to be faced. Tomorrow we have to be determined and focused and play a serious game.
"Then from game to game we will face everything as always, with maximum commitment and focused on doing our job well."
Motta began the season with a limited squad, still waiting on the club to bring in players, but the new coach now has plenty of options at his disposal, and Douglas Luiz and Teun Koopmeiners could both make their first starts next time out.
"They are two great players that I am lucky enough to have on our side, like many others in our squad. Let's see tomorrow who will start the game," Motta said.
"I'm happy because we have everyone available."
Empoli favourite Maccarone played at the Tuscan club when Sarri made his reputation there in a three-year stint that began in 2012, before the coach went on to Napoli, Chelsea and now Juventus.
Veteran boss Sarri only came to prominence in his early fifties, when Maccarone was a key figure in his Empoli side, just as Ronaldo now is at Juve.
And while 61-year-old Sarri has forged a plan to fit superstar Ronaldo alongside Gonzalo Higuain and Paolo Dybala in a three-man Juve attack, it was once the case that he had a quandary involving Maccarone.
Once he solved that puzzle, Empoli and Sarri went from strength to strength.
"At Empoli, the strikers were me and [Ciccio] Tavano, but he started with only one forward," Maccarone told Stats Perform.
"So, to let us both play – we were still young at 33 since we are still playing at 40 now, but still we were not so young – he adapted himself to the talent he had.
"This is when a manager proves to be smart. Ever since he changed the formation, we started getting points.
"Now he says, 'I have got Cristiano Ronaldo who will score at least one goal per game, so I have to adapt my style to his'."
Maccarone is a cult hero to many followers of Italian football, having returned from a spell in England with Middlesbrough to score regularly, largely for Siena and Empoli.
Still playing at the age of 40 for Serie C side Carrarese, he has fond memories of Sarri.
Maccarone and Tavano, who turned 41 last month, have taken their Empoli partnership to Carrara, where the veteran pair are again team-mates.
Sarri knew they were a potent partnership, which is why he ripped up his lone-striker policy at Empoli.
That flexibility was rewarded in the 2013-14 campaign when Empoli were promoted to Serie A, and a year later Sarri was on his way to Napoli, his home city club.
Looking back on Sarri's Empoli reign, Maccarone said: "At the beginning things didn't work out well, but there his style was born. I think he is one of the best managers I had.
"He gives you a lot of motivation and is a good talker. On the pitch you already know where, how and when you will receive the ball, then of course you have to add your spin.
"I like Sarri's way of playing football. When needed, he makes himself understood, he gets often angry because he wants everything perfect."
Juve struggled against the well-organised hosts, managing just three shots on target out of their 15 efforts, creating just 0.89 expected goals (xG) in the contest.
It follows another stalemate with Roma just before the international break, in which Juventus managed to test the goalkeeper just once.
"We barely got to the point of making the cross we wanted to make," Motta told a press conference.
"It's one thing to do it from behind and another to get to a dangerous area to do it. It's not easy with a team that defends like Empoli, we had difficulties.
"[But] not only Dusan [Vlahovic] has to fill the penalty area... We definitely have to improve on the sides and get to feed our attacker and those who come from behind."
Juventus' misfiring attack was not the only worry for the head coach, who made four changes to his midfield in the 67th minute.
Motta took off Manuel Locatelli, Nicolas Gonzalez, Douglas Luiz and Kenan Yildiz, introducing Khephren Thuram, Timothy Weah and Nicolo Fagioli, as well as striker Samuel Mbangula.
"They are great players and already in training with little time [they have had], they are able to understand what I want and how they should behave," Motta added.
"The four came in to give freshness. We didn't change anything on the tactical side, but we preferred to give continuity. Surely these players together on the pitch will grow, especially as a team."
Juve return to Champions League action after a season's absence on Tuesday, hosting PSV in the league phase of the revamped 2024-25 edition of the competition.
"Every game is different, the first two we faced [the way we wanted]. Today was a different game [to what it] will be on Tuesday, against a team that plays good soccer and attacks," Motta said.
"We have to be good at controlling the game, without allowing them to feel comfortable, because when they have the ball they always attack with many players."
The Rossoneri were held to a stalemate by the visitors to San Siro on Friday, missing the chance to consolidate their top-four spot after Inter had also drawn at Salernitana.
Having stunned the runaway title favourites Napoli 4-0 on their own patch last Sunday, Milan could not find the net this time despite having 23 shots, though only four were on target.
Pioli felt his side did all they could, but also suggested their performance reflected an anticipated comedown of sorts.
"It's not the result we wanted," he told Sky Sport Italia. "We had to do better in the first half. We played with great intensity.
"We conceded little to them, and in the second half, we did everything [we had to]. The ball just didn't want to go in.
"Goals are expected from the forwards if we create the chances. We needed to fill the area better. We lacked something to win.
"It's been a long time since we played with this level of energy and intensity, and I'm sorry. We wanted to win again after Napoli.
"But in my opinion, we're returning to the level [where we should be]. We need to improve our game, and we are doing that."
Milan face Napoli again next week, this time with the pair meeting for the first leg of their Champions League quarter-final at San Siro.
Milan are seventh in Serie A following Saturday's 3-0 win over Empoli at San Siro.
Reijnders scored twice, after Alvaro Morata had broken the deadlock, as Milan impressively put a defensively sound Empoli team to the sword.
But Milan are seven points back from league leaders Napoli, while they are six points off the top four.
"We haven't done anything yet, we have to keep pushing," said Reijnders.
"Good match but the points distance from the Champions League places weighs [heavily].
"We play to win [but] we are not satisfied with the position."
Coach Paulo Fonseca, meanwhile, credited his team's performance at both ends of the pitch, as they limited Empoli to zero shots on target and kept a fifth clean sheet in the space of seven home matches in Serie A this term.
"We played a great game against a team that is very aggressive defensively, which has the fourth-best defence in the championship," Fonseca told reporters.
"We played a very balanced game, offensively and defensively. There was one very important thing, the [quick] recovery of the ball in the offensive half of the pitch.
"We scored three goals but could have scored six or seven if we hadn't made the wrong last choices."
