Madrid came from behind to win 2-1 at Old Trafford on Tuesday and complete a 3-2 aggregate win after United winger Nani had been controversially sent off for catching Alvaro Arbeloa in the chest as he tried to control a high ball.
Ferguson shirked his media responsibilities after the match, while the home side’s players walked through the mixed zone without speaking to waiting reporters.
Assistant manager Mike Phelan faced journalists in the post-match media conference and he said the home side had felt betrayed by Turkish referee Cuneyt Cakir’s decision to send Nani off.
“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’m here speaking to you and not the manager of this fantastic football club.
“I think we all witnessed a decision which seemed very harsh, which seemed incredible in that moment of the game.”
Mourinho said United could have “no complaints” about Arbeloa’s reaction to the challenge, but said he had experienced a similar situation in 2011, when Pepe was sent off in a Champions League semi-final loss to Barcelona.
“(Nani’s dismissal) had the same influence as the decision two years ago to send Pepe off in the semi-final,” he said.
“At this level, there’s such a fine balance between such equally matched teams. Playing with one man down for such a long period is going to change a lot in the game.”
Ferguson unexpectedly omitted Wayne Rooney from his starting line-up but Mourinho felt the home side’s tactical set-up had been cleverly devised and said the United manager was beyond reproach.
“Sir Alex Ferguson has won the right (to pick his team) over the years,” he said.
“Every decision is correct and every decision should never have a question mark in front. He’s the best, he’s the top, he’s created an incredible history.
“You (reporter) are nobody, I am nobody, to put a question mark in front. His team was very well-organised. The defence was fantastic and I think he did a great job.”
United led 1-0 through a 48th-minute Sergio Ramos own goal when Nani was sent off and Madrid took just 10 minutes to level through substitute Luka Modric, before United old boy Cristiano Ronaldo netted a 69th-minute winner.
Modric has been unable to hold down a first-team place since joining Madrid from Tottenham Hotspur last year, but Mourinho praised his impact on the game.
“I’ve always been justified in bringing Modric to the club,” he said.
“I’ve always been fully convinced he’s a great player and today (Tuesday) he brought something different.
“Tactically, Man United were very well set up and defended stoutly, and Modric brought a bit of speed to our play with his vertical thinking. I think he made the difference.”
Mourinho conceded that he had also been indebted to second-choice goalkeeper Diego Lopez, deputising for the injured Iker Casillas, who produced a string of eye-catching saves in the closing stages as the visitors hung on.
“We couldn’t control the game with possession, which frustrated me, and in that moment we had Diego Lopez who gave us victory,” he said.
Phelan said United felt they “had got the tactics right” prior to Nani’s dismissal, but he said rousing the club’s players would not be a problem.
United lead Manchester City by 12 points in the Premier League and host Chelsea in the FA Cup quarter-finals on Sunday.
“Disappointment in football is part of the game,” he said.
“It’s important we finish the season well. We’re still in the FA Cup, we’ve got a great opportunity in the league, and I’m sure that’ll drive the players forward in order to achieve something.”