The two teams traded blows throughout a thrilling 90 minutes, but City claimed a 4-2 victory to book their place in the knockout stage.
City boss Pep Guardiola made four changes to the team that started against West Bromwich Albion in the league at the weekend.
Maurizio Sarri can feel aggrieved to have taken nothing from two pulsating encounters with City and his Napoli now face a must-win clash with Shakhtar Donetsk next time out to preserve their interest in the competition. Danilo replaced Kyle Walker in defence, while Ilkay Gundogan, Raheem Sterling and Aguero came in for David Silva, Bernardo Silva and Gabriel Jesus, who all dropped to the bench.
"Their matches have all been over by the 70th minute".
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15 minutes later and it was Napoli's turn to equalise as Jorginho levelled things up from the penalty spot.
Brook scored his final goal for the club in 1939, meaning Aguero has broken a record that had stood for 78 years. The Argentine then surged into the Napoli penalty box, and proceeded to power the ball home into the bottom right-hand corner, as he became City's all-time goalscorer with a whopping 178 goals to his name.
Napoli cleared the resulting corner behind but conceded from City's second attempt as Stones powered in Sane's outswinger via the underside of the crossbar.
City won the reverse fixture 2-1 at the Etihad and will expect a tough test at the Serie A side.