It is a rare admission by a manager, especially in such a high-profile match, that he sympathises with the losing side but Mourinho felt the 56th minute dismissal of the winger was as unfortunate as that of his player Pepe in the 2011 semi-final.
"In my opinion, the best team lost," the Portuguese coach, whose side went through to the quarter-finals 3-2 on aggregate after a 2-1 win on the night, told a news conference.
"I think it had the same influence as the decision two years ago to send Pepe off in the semi-final [defeat by Barcelona]," he added.
"When you are talking about football at this level, with such a fine balance between two equally matched teams, playing with one man down for such a long period is going to change a lot in the game."
In this encounter between two of Europe's biggest clubs, it changed everything.
United were leading 1-0 on the night, and 2-1 on aggregate, after a Sergio Ramos own goal but within 13 minutes of Nani's red card for an inadvertent high boot on Alvaro Arbeloa, they had conceded two goals to Luka Modric and Cristiano Ronaldo.
Mourinho felt it was right for Sir Alex Ferguson, who angrily remonstrated on the touchline and who was too upset to speak to reporters afterwards, to criticise the decision.
"I think I would always criticise," he said. "I think it's when you are talking about simulating... I can say for certain in this case Arbeloa was not feigning injury.
"It was quite strong contact from Nani on him and he was shown a red. On another occasion he could have seen a yellow for the same offence."
Mourinho said he had spoken to United manager Ferguson who had no complaints about Real's role in the incident.
It remains to be seen what the United manager, who has previously been in hot water for comments he has made about officials, will say about Turkish referee Cuneyt Cakir's decision to send his player off.
Ferguson opted not to face the media in the aftermath, sending assistant Mike Phelan to answer questions instead.
"Everybody was sitting in the dressing room wondering what had happened and why it had happened, a very distraught dressing room and a very distraught manager," he told a news conference.
"That's why I'm sat here."
He said that it was an understatement to say that Ferguson was not impressed with the red card.
"I don't think the manager is in any fit state to talk to the referee about the decision," he said. "I think it speaks volumes that I am sat here speaking to you and not the manager of this fantastic football club.
"We felt as though we had the tactics right for the game, for such a big occasion. We felt we were comfortable at times, at 0-0 it was where we wanted to be," he said.
"We came out and scored the goal which put us in a commanding position. After that we were in reasonable control, we created a couple of chances but then the game promptly changed.
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