The Portuguese trainer remained supportive of his compatriot despite a crucial miss in the shootout which saw his side eliminated from European competition on Wednesday
Los Blancos soared into a two-goal lead with a double from the Portuguese forward but Arjen Robben pulled one back for the visitors to make it 2-1, thus ensuring the tie would be settled from the spot.
Ronaldo, Kaka and Sergio Ramos all missed their kicks for Madrid, which enabled Bastian Schweinsteiger to secure Bayern's place in the final with a 3-1 shootout win. The 49-year-old trainer however remained supportive of his players, especially his highest scorer.
"Cristiano Ronaldo is fantastic. I will not compare him with [Lionel] Messi, we're talking about two great players. I will say this year Cristiano Ronaldo has been better," Mourinho declared in his post-match press conference.
He went on to praise the character of all of his players who stepped up to take a penalty, reminding those present that even the best can fail at times.
"The ones that miss the shot are the ones that have the balls to shoot. Fearless, not selfish, they go and try. I'm proud of my men.
"They're super men but Superman is a film. Messi missed yesterday [against Chelsea], and today three men missed because this is football, and these things happen."
"People criticise and question why these errors happen, people that if they climb two floors on ladders are exhausted.
"These guys worked like animals for two hours, they gave it all, then they go there and miss the shot."
Mourinho was also critical of the fact that while his team were forced to play a potentially title-deciding fixture against Barcelona on Saturday, Jupp Heynckes was able to rest eight key players for their visit to Werder Bremen with the Bundesliga title out of reach.
"Both of them [Bayern and Chelsea] used their second squads this weekend, and they played versus Barca and Real, who played the most important match of the domestic season last weekend.
"It's our fault. If we were not playing for La Liga we would have not lined up our best men last Saturday.
"[It is] very difficult to stay in more than one competition. The final of the Champions League will be played between the fifth team of the Premier League and the second of the Bundesliga, [who are] 10 points behind [the league leaders]."
Los Blancos will now look to bounce back from defeat and secure La Liga, starting when they welcome Sevilla to the Bernabeu on Sunday at 12:00CET.