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 with a 2-1 victory.
Chelsea have now recorded four consecutive home victories in the Premier League, and head into 2014 just two points adrift of leaders Arsenal in third place.
"I keep saying there is a big difference between Manchester City and the other teams," he said.
"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 favourites, 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)."
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 counter-attack situations where we could have killed the game.
"We didn't (do that) and until the last minute it was hard, but we deserved (to win)."
