Mourinho, who received abuse from the home fans throughout, still found time to criticise referee Phil Dowd, with whom the Portuguese fell out on a few occasions during the match.
"Was the referee very poor in the second half? Yes," Mourinho said.
"But even with a perfect referee would Chelsea win? No. The second goal was offside but we were never close to being dominant.
"City played much better than us and they deserved to win. Two weeks ago the best team won and it was the same here. When the best team wins I think football is in peace."
Mourinho, who has admitted he wants to sign a forward in the summer, kept his frustrations regarding his misfiring strikeforce to himself after the match.
"There are things I cannot say," Mourinho said when asked about his team's troubles in front of goal this season.
"There are things I can just think and keep to myself. I don't want to individualise to speak about my striker or my keeper or my left-back. We are a team, we win, we lose."
"No, it was not revenge,” he said. “We didn't want to lose two games against Chelsea here at home. The team played very well in all senses.
“We saw again the team that was playing before the last two games. It was very important for us to lose three points in the Premier League against a very good team with great players.
"The way we won today is important for the trust of the team, for continuing in the FA Cup. For our team it is a very important competition also, but nothing more."
The result kept alive City's challenge in four competitions but Pellegrini was not interested in discussing a potential quadruple.
"We never talk about that. We try to fight in all the competitions as far we can,” he said.
"It is one step more but we continue now in Champions League."