The Premier League leaders ultimately claimed a 3-1 victory, with Diego Costa, Willian and Eden Hazard all finding the net in the second half after Gary Cahill's own goal had gifted City the lead on the stroke of half-time.
And to compound a miserable afternoon for the home side, they lost both Sergio Aguero and Fernandinho to red cards as tempers flared over in stoppage time.
Kevin De Bruyne had earlier hit the crossbar from just three yards out when his side were 1-0 up, while Aguero had also gone close and Fernandinho's headed effort was correctly ruled out for offside.
And it was those near-misses that Guardiola felt cost his side dear.
"It was a very good performance from us and we created a lot of chances," he told reporters. "We had a lot of the ball and created enough chances to win the game, but we were not strong enough in the box.
"De Bruyne should have scored, but we did not lose the game because of that particular bit of action. There were many incidents. We created two or three more chances after they went 2-1 up.
"They had three chances and scored three goals and that is a huge talent. In the box, they are so strong.
"Our level was quite good, I'm so proud of how we played. We created more chances than we did against Palace and Burnley.
"But football is all about goals, conceding them and making them and ultimately Chelsea are right and we are wrong because they won and we lost."
Guardiola refused to criticise Aguero, who was sent off deep for a dangerous lunge on David Luiz that left the Brazilian writhing on the ground.
But the Spaniard did express regret over the ensuing touchline fracas which culminated in Fernandinho also being dismissed.
"Both players went in strong and that's it," he added. "It's a pity it finished like this. I don't like that. I apologise for what happened."
The result marked a first home league defeat for City under Guardiola and leaves them four points adrift of Chelsea, who consolidated their position at the top of the league with what was their eighth straight top-flight win.