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City were superb for much of the match but goals from N’Golo Kante and David Luiz undid our good work and saw us lose for the first time in the Premier League this term.
The result means we now sit second in the table, one point behind new leaders Liverpool.
But Stones believes there were plenty of positives to take from the game, and says he is delighted with how the first 16 games of our title defence have gone.
"To come here and play how we did, despite the scoreline, is never easy,” he said.
“We were top of the league coming into the game and everyone wants that spot. Now we have something to look back on and we will take everything out of it.
"It is never easy to digest it after the game, but it is the harsh reality of the league. To be where we are - we should be proud."
City play Hoffenheim in the Champions League on Wednesday, before resuming Premier League duties at home to Everton next Saturday.
Indeed, we are currently in the midst of a run of 14 games in 44 days spanning three competitions.
It’s a crucial period for City and Stones says bouncing back from defeat at Stamford Bridge is critical.
“We should take positives into the next game,” he said.
“The best way to get over this is by winning the next game.”
"It was a typical game between two top teams. It is not easy conceding late in the first half. We were so dominant, but they got one chance and scored it.
"It is frustrating but that is the reality of playing these top teams in the Premier League. We did everything right up until the last minute.”
Stones went head-to-head with Eden Hazard, who played as a centre-forward rather than occupying his usual wide position.
And alongside Aymeric Laporte, Stones handled him superbly, minimising the Belgian's impact on the game.
"I have played against him quite a few times over the summer and at the start of the season,” Stones said.
“Both teams tried to switch it up to try different tactics.
"As a back four, in controlling Hazard we kept them from creating a lot of chances.”
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