A blistering start from City resulted in Raheem Sterling and Gabriel Jesus putting the team 2-0 ahead, but their Italian opponents could have got something out of the game had Dries Mertens's penalty not been saved by Ederson.
The Serie A outfit managed to get on the scoresheet in the second half when Amadou Diawara netted from the penalty spot, but it was City who came out on top.
"We've put ourselves in a good position, a lot of games to play still. I say it all the time but we've got to keep going game by game," Stones told reporters after the game. "I think tonight was a great test to see where we were really at after a good run of hard games. We knew it was going to be a tough test.
"We wanted to play our game and I think some of the football out from the back right the way through to the guys up top was, at times, great to watch for me personally. We're a bit upset to concede the goal that we did, I thought it was a bit soft but overall a great team performance.
"Every game is a hard game. We want to keep improving, keep scoring goals, keeping clean sheets and hopefully we can progress in the group."
As it stands, City sit at the top of Group F with a three-point advantage.