The Premier League champions led 2-1 at Stamford Bridge on the opening day of the season after a Federico Fernandez own goal cancelled out Andre Ayew's equaliser, following Oscar's opener.
But goalkeeper Courtois was given his marching orders by referee Michael Oliver early in the second half for bringing down Bafetimbi Gomis and the striker put the resulting penalty past substitute Asmir Begovic.
Mourinho would not be drawn on whether or not Oliver made the correct decision, but said the dismissal forced his side on to the back foot.
"We played very well until we played with 10 men," Mourinho told Sky Sports. "In the first half I think we played with high quality.
"In our game with 10 men we fought hard for a long time. It was not five, 10 minutes, they fought hard.
"I don't want [to make a comment on the decision]. You [the media] have the cameras, you have the pundits, the specialists, I don't want to comment.
"We played very well in the first half, the game was under control, the players were playing with more and more confidence. Oscar was playing a lot, Willian as well. The midfield was confident.
"Then after the penalty, red card, goal, everything is different. We fought hard, in some moments we had to defend and fight hard and not to lose the game.
"In other moments of that period with the set-pieces, counter-attack we could have scored a goal. The game was open."
