On a night when Kalvin Phillips returned to action to stake his claim for a World Cup place, City prevailed at the Etihad Stadium with second-half goals from Riyad Mahrez and Julian Alvarez.
Manager Guardiola said: "Knowing the opponent and the quality they have, I am more than pleased. I am happy for all the performance of the players.
"We suffered because they are so good. When they gain the ball and they drive 40 metres we cannot defend that, they are really good.
"It doesn't matter what happened in their last results, they are a fantastic team and I am happy to be in the next round."
Phillips played 40 minutes in his first appearance since undergoing shoulder surgery in September.
With England manager Gareth Southgate due to name his World Cup squad on Thursday, it was the midfielder's final opportunity to prove his fitness for the tournament in Qatar.
"It was an amazing feeling," Phillips told Sky Sports. "It's been a long time but I'm just glad to get back out there and play with the lads.
"Without playing football for a while it is going to be nerve-wracking when you step onto the pitch, especially for one of my first appearances for the club. So, it felt good but it made it a lot easier with the two goals that went in.
"I'm back fit now so hopefully I've got a chance."
Phillips, who joined City from Leeds in the summer, had played just 14 minutes of football prior to his operation this season due to other fitness issues.
Guardiola said: "Kalvin made a good 40 minutes. He didn't play for a long time but he played with incredible personality.
"Of course he has to get some things, that is normal, but in the second part of the season we need him because Rodri cannot do it all the time."
Both of City's goals came in a five-minute spell early in the second half, giving them a control of the game they did not relinquish.
Yet Chelsea caused the hosts problems at times and, after defeats in their last two Premier League games, manager Graham Potter was pleased with the display.
He said: "I thought there were quite a few positives. Obviously we are disappointed with the result but in terms of how we played, we created some good chances and there was a better structure and a better performance level.
"The team looked closer to what we want it to look like. The boys had great courage and they tried against a top team.
"Their keeper got the man of the match I think, which tells a bit of the story. But overall I think it was a step forward for us."