Mourinho consoles Frank Lampard and John Terry
Chelsea's 1-1 draw with Arsenal at the Emirates ensured United claimed the title for the first time since 2003.
"I have to say maybe I'm prouder now than when we were champions," said Mourinho. "All season my players have been heroes against everything.
"This was a game to remember and showed how big Chelsea are as a club."
Mourinho offered his congratulations to Manchester United, but could not bring himself to say that the best team had won the title.
"It doesn't matter, what matters is the team with more points is the champion," added Mourinho.
"I have to congratulate the champions, the players, the manager, the fans, the board; all the people that helped them to be champions.
Mourinho pinpointed Chelsea's lack of defensive cover for centre-back Ricardo Carvalho as why the defending champions had failed to win the Premiership for a third successive time.
"We had a big problem only to play all season only with Carvalho at centre-half but now is not the moment to talk about that.
"I'm very proud of my players. Normally when a team has a lot of success and loses a championship it's lack of motivation, not the same spirit or ambition, but it was exactly the opposite."My team was brilliant."