Not only did the goal put City ahead again on the night, it also made Aguero City's all-time record goalscorer.
City boss Pep Guardiola made four changes to the team that started against West Bromwich Albion in the league at the weekend. John Stones rose highest to meet Leroy Sane's cross and power a header past Pepe Reina to make it 2-1. The first shot of the match eventually came from Marek Hamsik in the sixth minute, although his effort was comfortable for Ederson.
Indeed, it was the home side that made the breakthrough in the 21st minute when Insigne played a one-two with Mertens inside the City box before finding the back of the net with a super finish.
Napoli probable XI: Rina, Hysaj, Albiol.
City started the second half just as they finished the first, scoring from a corner kick.
City won the reverse fixture 2-1 at the Etihad and will expect a tough test at the Serie A side.
Manchester City's Nicolas Otamendi, back to camera, celebrates with teammates after scoring tonight.
Sane then redeemed himself with a brilliant individual effort on the counter-attack, running the length of the field and losing the ball only for Sergio Aguero to recover it and score the victor.