Despite scoring two goals on the night, Ronaldo missed his penalty in the shootout which was won 3-1 by Bayern to set up a final with Chelsea.
However, Mourinho believes that Ronaldo's form for the team has been vital this season and instead chose to praise the former Manchester United winger.
Mourinho said: "Cristiano had to fail someday.
"I don't want to be radical and say if he or someone else is the best, I do not want to go there. We are talking about Messi and Cristiano, two unique players.
"But this season, Cristiano has been better and a difference-maker. If Barca and us have not made it to the final, it is both our fault. After two hours of working to our limit, going to penalties is not easy. The luck was with them."
Despite Los Blancos' exit from the Champions League, they are currently on course to secure the La Liga title.