Ex-Blues star Kevin De Bruyne came back to haunt his former club by scoring a stunning goal at Stamford Bridge to secure City’s 1-0 win.
Both clubs were involved in Champions League action during midweek with City beating Shakhtar Donetsk at home and Chelsea claiming a superb win away to Atletico Madrid.
Chelsea played a day later than their opponents today and Conte says his side’s lack of recovery led to their loss.
He said: “It was a tough game but we know very well that Manchester City are a big team and it's very difficult to play this type of game.
"I think that we gave everything today and I am happy with the commitment and desire from all my players. They had the will to fight against a very strong team.
"In this type of game you need time to recover, if you are tired it is not simple to go box to box.
“Today we created chances but we didn't take them. Manchester City had chances and they took them.
"It is logical when you play three games in seven days you risk something. I hope it is not a serious injury for Morata. It is his hamstring but we don't know if it is a serious problem.
"We move on, we rest and I am very proud to be the coach of these players."
Chelsea legend Frank Lampard was not impressed with how his former club performed against City.
He said: “[Chelsea were] outclassed, outplayed, they were out-positioned.
“Every Man City player on the ball had three or four options.
“Chelsea were two or three seconds late on the press, they never got close as a team.
“Once you continuously do that for a game, eventually with the quality Man City have, they’re going to produce a moment of quality which Kevin De Bruyne did.”
The Chelsea and City stars will now leave for the upcoming international break.
Chelsea face Crystal Palace while City host Stoke when the Premier League resumes on October 14.
