City dominated possession early on at Stamford Bridge, but could not find a way through a well-organised Chelsea defence and were hit on the break just before halftime as N'Golo Kante netted Chelsea's first shot at goal.
Guardiola, however, still liked what he saw, believing Chelsea simply took their chances at key moments.
"If they have one chance they will score one goal because the opponents are so good and determined.
"That is what's going to happen in the future on the biggest stages but the way we played today was incredible. I'm delighted. We were outstanding except for five to eight minutes.
"We try to be champion. Everyone wants to beat us. Now it is recovery for the Champions League."
Despite having over 62 percent possession, City mustered just one shot on target before the interval, and were forced to chase the game in the second after Kante's goal.
They looked unusually ineffective though and never really looked likely to salvage anything after Luiz's late header.
After defeats by Tottenham Hotspur and Wolverhampton Wanderers in their last three matches after going unbeaten in their opening 12 league games, it was a return to form for Chelsea after the first serious questions had been asked of new manager Maurizio Sarri.
He said the change of emphasis from a possession-based game to a counter-attacking style had been key against City.
"Yes, of course (it was the intention to be more defensive)," Sarri said.
"We know very well that the ball possession is usual for us, today was a problem and so we knew very well that maybe there were more spaces for counters.
"We defended very well and then we started to press better and after the first goal the match changed and we played well in the first 20 of the second half, and in the end we deserved to win and I am happy with it.
"It's not easy to win against Man City." (Reporting by Peter Hall; editing by Martyn Herman)
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