Real had midfielder Pepe sent off after 62 minutes and Mourinho was sent to the stands for his protests soon after, and Lionel Messi took full advantage to score both goals in a stunned Bernabeu.
"Congratulations to a fantastic football team," the Real coach said in a rambling rant at the post-match news conference.
"But congratulations for all they have as well, it must be difficult to get to get all this power. Where does this power come from? I don't know if it's because they give UNICEF publicity (on their shirts)?"
Mourinho went on to list Barca's semi-final victory over Chelsea in 2009, the Inter Milan semi-final from last season and now "the scandal of the Bernabeu," as he suggested unfair red cards had been issued to rivals playing the Catalan side.
"This thing happens in each semi-final," he said. "I am here just to ask this question and I hope to get the answer one day.
"I respect him (Barca coach Pep Guardiola) a great deal as a coach and a person... but I would like to see him win a Champions League without scandals.
"Pep is a fantastic coach and he has won one Champions League. I would be ashamed to have won it after the scandal of Stamford Bridge (when he said Chelsea should have had four penalties).
"I won two Champions Leagues with Porto and Inter and won both on the pitch. We won with work, effort, sweat and fight."
The second of those European crowns came after a famous rearguard action with 10 men at the Nou Camp last season, losing 1-0 after having won the first leg 3-1.
However, Mourinho quickly ruled out any chance of another heroic performance in next Tuesday's second leg at Barca's stadium.
"Obviously in the return leg it's a very difficult mission," he added. "It's not very difficult, it's impossible.
"They will get to the final and that's that"
Real have had a player sent off in each of the four 'Clasicos' they have played in La Liga, the King's Cup final and the Champions League this season, and now will be without the suspended Sergio Ramos and Pepe next week.
Mourinho, who said he was not supposed to be speaking to the media after having been sent off, will have to watch from the stands.
When asked what he had said to receive the punishment from the German referee, Wolfgang Stark, he replied: "I didn't say anything, I just applauded his decision with two thumbs.
"If I told UEFA and him what I thought and feel I would end my career now."
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