The Chelsea manager watched his side negate City's attack - which had found the net in their last 61 top-flight home games - and inflict a first domestic defeat of the season at the Etihad Stadium on Manuel Pellegrini's men.
Branislav Ivanovic's goal in the 32nd minute of the match proved enough to secure all three points, but Chelsea - who beat City 2-1 at Stamford Bridge in the reverse fixture - refused to sit back on their lead and hit the woodwork on three separate occasions.
And Mourinho was delighted to see his team produce such an effective performance, hailing the three points as a crucial milestone in Chelsea's development.
"I think we played fantastic, to play the way we did is amazing," he told Sky Sports. "In this process of building the team to be one of the favourites for next season this is a very important step.
"The best team in the Premier League - we beat them twice, today we were fantastic.
"We had the better chances to kill the game, the players played with fantastic spirit. When they had the ball we were very humble and ready to work defensively, when we had the ball we played and played really well."
The victory moves Chelsea level with second-placed City in the Premier League table, just two points behind leaders Arsenal, but Mourinho refused to label his side one of the title favourites this season.
"We are there, but not favourites," he added. "For the team it's very important, the feeling is fantastic feeling for them.
"Today we won because we were the best team, not better than them but today they were fabulous.
"It is not our objective to win (the title this season), our objective is to build the team and complete the formation of the players.
"I want to start next pre-season and say this season we are going to compete and be one of the favourites."
