Barca won 2-0 at the Bernabeu on Wednesday to take a decisive step towards the Champions League final in an ill-tempered game that saw Real reduced to ten men for the fourth successive El Clasico.
And Mourinho made it clear in an astonishing post-match interview that he felt Wolfgang Stark had not only made a serious error but was the latest in a long line of officials to favour Barcelona in big games.
Ronaldo echoed his manager's sentiments, insisting that his Portuguese compatriot's dismissal was unfair.
"I do not understand why everyone playing against them (Barcelona) in the Champions League ends with ten men, Arsenal, Chelsea... It is not an excuse but playing against ten is very different to playing with 11.''
Asked whether he had quizzed the referee after the game, Ronaldo said: "If I had tried to talk to him I would have got a yellow card. We are sad in the dressing room because every year is the same.
"We controlled the game at 11 versus 11 but we conceded two goals when we were down to ten. Every year is the same and I do not understand. The truth is that getting through the tie is now very difficult, but in football anything can happen.
"A goalless draw would have been a good result. We had a strategy. At the end Kaka would play a few minutes and we were going to attack. Football is all about strategies.''
Aside from last week's Copa del Rey final, in which Ronaldo scored the winning goal, the former Manchester United star has been upstaged time and again by Lionel Messi when he has faced him.
And Wednesday night was no different for a frustrated Ronaldo, with Messi's two goals at the Bernabeu taking him to an incredible total of 53 in 52 games this season.
Ronaldo refused to credit the two-time World Player of the Year, though, saying: "I wish I had the chance as Messi did to play against 10 because then everything is so much easier."
Ronaldo's team-mate Xabi Alonso accepted Madrid were now up against it as they look to battle back at the Camp Nou and set up a probable final clash with Manchester United.
"Pepe's dismissal changed the game," Alonso told TeleMadrid. "We will go to the Camp Nou in a professional way but it is complicated.
"We prepare for games like this all season and the referee has got it wrong. I am biased but I did not think it was a red card.''