The Portuguese believes Manuel Pellegrini's side has the edge in the battle for the Premier League title.
Mourinho saw his team overcome Martin Skrtel's third-minute opener at Stamford Bridge, as Eden Hazard's curling strike and Samuel Eto'o's finish from six yards secured all three points in a 2-1 victory.
Chelsea has now recorded four consecutive home victories in the Premier League and heads into 2014 just two points adrift of leader Arsenal in third place, but Mourinho believes second-placed City remains the team to beat.
"I keep saying there is a big difference between Manchester City and the other teams," he told reporters. "It's not just about quality, other teams have quality, us too. But [it is about] maturity, the number of players, the group of strikers, physicality, experience.
"They [City] are the favorites, for us, for Arsenal, for Liverpool, to be around [the top] is a good achievement. In our case it's important people learn how to play these matches [against the top sides]."
Mourinho felt his side was good value for its victory on Sunday and was particularly happy with the way it bounced back from an early setback.
He added: "I think we deserved to win because they did nothing to score the first goal, it was circumstantial. After that our reaction in the first half was a fantastic reaction. We scored, we could have scored before.
"In the second half we defended well, they hit the post with [Mamadou] Sakho, we had some counterattack situations where we could have killed the game. We didn't and until the last minute it was hard, but we deserved [to win]."
Mourinho also confirmed midfielder Frank Lampard is set for a spell on the sidelines with a muscular injury, but is hopeful the lateral ligament issue picked up by Branislav Ivanovic is not serious.