Raheem Sterling and Gabriel Jesus scored inside the first 13 minutes at the Etihad Stadium to put the hosts in charge during an impressive performance on Tuesday.
Amadou Diawara netted from the penalty spot in the 73rd minute to give Maurizio Sarri's visitors hope of snatching a point.
But City held firm to lead Group F by three points from second-placed Shakhtar Donetsk, leaving Stones satisfied with another strong showing.
"In terms of the group I think we've put ourselves in a good position but we have got to keep going game by game," the defender said.
"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 an 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."