The England international being benched means Manuel Akanji starts on the right of a three-man defence
Napoli defender Kalidou Koulibaly returned from the two-match ban he received a month ago after being targeted by racist chanting by Inter Milan fans at the same San Siro stadium.
Anti-riot police took up positions around the San Siro as part of stringent security measures Saturday, but the match took place without incident apart from some anti-Neapolitan songs beforehand.
Napoli's Lorenzo Insigne also returned from suspension and formed a four-man attacking line-up along with Dries Mertens, Arkadiusz Milik and Jose Callejon.
"It was a totally different atmosphere and this is what we want to see in the stands. I applaud all the fans," said Ancelotti.
Italian Interior Minister Matteo Salvini said it had been the right decision not to limit ticket sales or access to the stadium.
"Happy that #MilanNapoli was played nice and quiet, outside and inside the stadium," tweeted Salvini, a passionate AC Milan fan.
On the pitch most of the action occurred in the final half an hour.
Napoli finished with ten men after Fabian Ruiz received a second yellow card in injury time for a disputed handball, with Ancelotti banished from the sidelines for swearing.
Both goalkeepers pulled off saves with Gianluigi Donnarumma denying Napoli's Callejon after six minutes, and David Ospina saving a point-blank Mateo Musacchio volley.
The two sides meet again in Milan on Tuesday in a Coppa Italia game.
Second-placed Napoli stay eight points behind champions Juventus who travel to Lazio on Sunday, while Milan, in fourth, missed a chance to close the gap on city rivals Inter, and could be overtaken by Roma who play Atalanta.
"Napoli are an opponent who always keep you on your toes and had all their forwards out there today," said Milan coach Gennaro Gattuso.
"We began to get stretched out in the second half and were struggling with fatigue, but I am happy with a good point."
Earlier, Sampdoria forward Quagliarella bagged a brace to equal Gabriel Batistuta's record of scoring in 11 consecutive Serie A games, in a 4-0 win over Udinese.
Quagliarella, who turns 36 next week, matched the mark after converting a penalty after 31 minutes, and added a second, again from the spot, on 56 minutes.
The evergreen forward also had a role in the other two goals - in the build-up to Karol Linetty's third on 68 minutes, and the decisive cross for Manolo Gabbiadini to tap in ten minutes later.
"I'm speechless, just naming Batistuta gives me goosebumps," said Quagliarella.
"I kept thinking with every game that the run would surely be interrupted, but it kept going."
Batistuta scored at least one goal per game in the opening 11 games of the season in 1994-1995 for Fiorentina. The Argentine went on to finish the campaign as the top scorer with 26 goals.
Quagliarella has had one of the best seasons of his career with Sampdoria.
He has scored 14 goals in his 11-match run for a total of 16 this season, to go top of the Serie A scorers ahead of Juventus star Cristiano Ronaldo (14).
The 25-times capped Italian international scored a career best 19 goals last season.
Sampdoria moved up to sixth, the final Europa League berth, and just two points off the Champions League places.
Sassuolo shrugged off the shock departure of Kevin-Prince Boateng to Barcelona by ending their four-month home win drought with a 3-0 success over Cagliari, keeping their Europa League push alive.
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