Branislav Ivanovic was the hero for Chelsea with a brilliant strike as they ended City's perfect record at the Etihad Stadium with a superb display.
The victory moved Mourinho's men level on points with City and two adrift of leaders Arsenal, but the Portuguese insists he is not planning on winning the Premier League this term and is building for next season.
"I think we played fantastic, against a fantastic team. To play the way we did, I think is amazing for the boys in this process of building the team and prepare the team to be one of the favourites next season," Mourinho told Sky Sports.
"I think this is a very important step - the best team in the Premier League, we beat them twice (home and away), and especially today we were fantastic.
"They had a couple of chances to score but we had the better chances to kill the game and the players played with fantastic spirit - the way I was trying to explain.
"You never know how things go but when they had the ball, we were all very humble and all very ready to work a lot defensively.
"When we had the ball, we were trying to play and we played very well."
Mourinho insisted, despite the manner of his side's victory, they are not favourites for the title and claims he is only thinking about the long-term development of his players for next season.
"We are there, but we are not favourites" added Mourinho.
"I just think it is very important because it is not good for the evolution of the team if you are playing in the Premier League 10, 15 points behind the leaders.
"It is not good for the evolution of the team if you are playing Europa League. We need big things... we need these kind of matches with the pressure we felt today and this for the team is very important."
Mourinho refused to pick out individuals, admitting it was a real team performance that enabled Chelsea to come away with all three points.
"I think they did amazing," he continued. "When the team needed Petr (Cech), he was there, Ivanovic as a defender to score that goal is fantastic, the central defenders were immaculate.
"Azpilicueta was up against Speedy Gonzales, because Jesus [Navas] is unbelievably fast, but he did a fantastic job. The midfield players worked fantastic and the attacking players were always dangerous and when the team lost the ball, they all sacrificed for the team and everyone gave a great contribution."
Despite getting the better of City twice this season, Mourinho is refusing to get carried away, but says the victories will be important for his side's mentality.
"The record was not good against them in the last years," he admitted. "This season, we managed to win these two matches in the Premier League - the first one we won basically because Nando [Fernando Torres] was so smart, so clever in that last ball in the game, and today we won because we were the best team.
"But I am not saying we are better than them, I am not saying that. I am just saying we were better and the boys deserve the victory."
Asked why he was not championing his side's title chances, Mourinho added: "Because it is not our objective to do that, our objective is to build a team. Our objective is to complete the puzzle and, more than the puzzle, complete the formation of the players.
"Some managers, some clubs because of their nature, their DNA say I need two, three, four, five years. I want to start the next pre-season in the summer and to say, and also my players to say, that this season we are going to compete directly with the best and we consider ourselves one of the favourites.
"This season, I'm sorry I can't do that."