Victor Osimhen’s bullet header sparked a nervy finish to the tie but Milan did enough to advance to the semifinals at Napoli’s expense.
City are chasing their first-ever Champions League trophy but will have to navigate past another German team in the knockouts if they will remain in contention.
Osimhen is the first Napoli player to score in both legs of a Champions League knockout game.
Real Madrid demolished Liverpool on Tuesday night, leaving Anfield shell-shocked.
Juventus can still appeal the decisions handed down by the Italian football federation.
The Super Eagles forward put Napoli upfront in the 14th minute with a header from a Khvicha Kvaratskhelia rebounded overhead kick.
Osimhen leads the Serie A top-scoring chart with 10 goals, and he is the only player to achieve a double-figure goal tally in the league this season.
Osimhen scored his ninth goal of the season as Napoli beat Isaac Success’ Udinese 3-2.
With 32 goals so far, Osimhen has become the highest scoring Nigerian player in Serie A history, surpassing Simeon Nwankwo’s 31 goals.
Mohamed Salah scored a six-minute treble as Liverpool thrashed Rangers 7-1 at the Ibrox Stadium.
