A high quality match at the Etihad against the Italian league leaders went City's way thanks to early goals from Raheem Sterling and Gabriel Jesus.
City were indebted to goalkeeper Ederson who saved a first-half penalty from Dries Mertens. However, Napoli did successfully convert a second-half spot kick through Amadou Diawara to set up a nervy last 20 minutes.
City stayed solid to secure a third successive Champions League win to sit three points clear of second placed Shakhtar Donetsk at the halfway stage.
"In terms of the group think we've put ourselves in a good position but we have got to keep going game by game," said Stones.
"Tonight was a good test to see where we are at against what is a very good team.
"There are a lot of games to play still but this was a good test for us.
"Every game is a hard game and we've got to try to keep improving, to keep scoring goals and to trying for clean sheets.
"They put a lot of runners in behind. We knew they played patient football and had attacking threat. We knew it would be tough but we wanted to play our football.
"At times it was great to watch. I am upset to concede the goal we did but overall a great team performance."
Stones' defensive colleague Kyle Walker also had words of praise for goalkeeper Ederson who crucially saved a first-half penalty.
"We knew they would come at us in the second half but the lads showed good character. Ederson has kept us in it," said the right back.