The Portuguese star didn't make an appearance until the 83rd minute of the game which ended in a 2-1 win for the La Liga giants.
Mourinho said: "We were playing against a team of fantastic players and we discussed the result until almost the end, not the end but almost the end.
"Almost the end because when Cristiano Ronaldo is coming, the referee decided to show the respect for this amazing player, and then game over because every time Cristiano wanted a free kick the game was stopped.
"But we gave them a fight, we gave them a good fight and my boys only have reasons to leave - okay, disappointed because to lose is disappointing - but to leave optimistic and proud. Let's go for it on Sunday."