City entered the match knowing that a point would be enough to book their spot in the round of 16, but they collected all three on a night where Sergio Aguero became the club's all-time leading goalscorer on 178 goals.
"Their matches have all been over by the 70th minute".
Both teams had their moments in what was a very lively first 15 minutes, but Napoli were creating the better chances - Mertens firing at Ederson from a wide angle after another smart move.
Manchester City's Nicolas Otamendi, back to camera, celebrates with teammates after scoring tonight.
Five minutes into the second half Stones did find the back of the net for City when he met a corner-kick with a powerful header that beat the Napoli keeper, 2-1.
City overcame Napoli 2-1 in the reverse fixture at the Etihad Stadium, but it was a tough game and the sequel, in Naples, promises to be even more challenging for Pep Guardiola's men.