Having branded Arsenal boss Arsene Wenger a "specialist in failure" after eight years without a trophy as the mind games ramped up in the Premier League title race this week, the Portuguese was given a taste of his own medicine at the Etihad Stadium on Saturday as his side were outclassed.
Mourinho's men had completed a league double over title rivals City with a 1-0 success on the same ground 12 days earlier, but they found themselves second best on this occasion as City eased into the quarter-finals.
Goals from Stevan Jovetic and Samir Nasri, whose effort was allowed to stand despite a suspicion of offside in the build-up, ensured progress for the hosts.
And, while Mourinho conceded that Chelsea had been outplayed by a comfortable margin, he was quick to defend his team's showing amid questions over whether this result represented a failure of his own.
"I don't think my team failed," Mourinho said. "City played much better than us, deserved much more than us to win. When the best team wins I think football is in peace.
"Two weeks ago the best team won, and today the best team won. That's simple and gives more credit to my players because to win twice against City, and to win here, today (Saturday) it was proved that it is very, very difficult to do it.
"Was the referee team very poor in the second half? Yes. But even with a perfect referee team would Chelsea win the game? No.
"They were better than us, they deserved to win. The second goal is offside, but they would win 1-0 because we were never close to scoring."
Mourinho also dismissed suggestions that Chelsea's FA Cup exit could serve to boost their Premier League title chances, insisting that the extra games would not have an impact on City, who also play in the League Cup final against Sunderland on March 2.
"We go game by game, we are what we are, we always try to win the next game," Mourinho added.
"I don't think one more game or two more games in the FA Cup would change anything for us or anything for them, especially with the powerful squad they have, so I don't think there is a problem."
