The Real Madrid coach sympathised with a furious Sir Alex Ferguson after a controversial red card for Nani proved the turning point for Real's 2-1 comeback victory.
Champions League: Man Utd did not deserve to lose, admits Jose Mourinho as Real Madrid reach quarter finals
Manchester United 1 Real Madrid 2
(Madrid win 2-3 on aggregate)
Man Utd: Ramos 48' (og)
Real Madrid: Modric66', Ronaldo 69'
Ten-man Manchester United were left seething after crashing out the competition in controversial fashion following the sending off of Nani.
The home side were 2-1 up on aggregate after an own goal before the red card, handing a lifeline to Madrid which was exploited by Luka Modric and Cristiano Ronaldo - scoring on his return to his former side.
But afterwards Mourinho said he felt his side were still lucky to get through.
"I try to be honest," he said. "In my opinion, the best team lost. That is football.
"When we were against 10, we played very well for 10 minutes. We gave them a new problem they couldn't solve.
"But I know Old Trafford and what Sir Alex Ferguson could do. We couldn't control the game by possession. That frustrated me."
Sir Alex Ferguson left Wayne Rooney on the bench and tasked 39-year-old Ryan Giggs, playing his 1000th game for United, with shackling former teammate Ronaldo.
The Welshman excelled in his role, while Danny Wellbeck offered a significant threat to Real with his runs from deep.
Real struggled to find a way through to the United goal during the early exchanges. Gonzalo Higuain sent a decent chance wide in the opening stages but other than that, there was always a home defender in the way.
Ronaldo, after his heart-touching reaction to the reception he received, was extremely subdued, failing to make any impression with a free kick perfectly located for one of those jaw-dropping efforts he seems to have made an art form.
The loss of Angel Di Maria just before the interval forced Mourinho into a tactical reshuffle which Real were still adjusting to when United struck.
Rafael's surge to the edge of the box had Real floundering and although Robin Van Persie's shot was deflected away from goal, Nani had the awareness and strength to shrug Raphael Varane off it.
Welbeck got the faintest of touches to the Portugal winger's cross but it was enough to ensure Ramos' was firm enough to send it rolling into the net.
But United's joy was to be short-lived, as referee Cuneyt Cakir made his presence known.
When Nani challenged Alvaro Arbeloa for a bouncing ball inside his own half, he seemed committed and nothing more.
Cakir deemed it dangerous and after waiting until the winger recovered from a non-existent injury, out came the red card.
United tried to hang on but it took the visitors just 11 minutes to turn the entire tie on its head.
Modric struck first, with a viciously curling effort from 25 yards.
Three minutes later Mesut Ozil found Higuain, whose cross was turned home at the far post by Ronaldo.
Rooney's introduction saw him handed a chance to equalise, but he lifted over the bar from six yards out.
Mourinho sympathised with United over the referee's decision, although insisted that Arbeloa had not dived.
"I can say for certain Arbeloa did not feign contact," he said. "It was quite strong and he was shown a red. It could have been a yellow."
And the Real Madrid manager, long tipped as a successor to Ferguson at Old Trafford, defended his opposite number's decision to leave Rooney on the bench.
"Sir Alex has won the right for every decision to be correct and never have a question mark against them," said Mourinho.
"He is the best. He is the top. You are nobody to put a question like that. I am nobody.
"He did a great job."
Mike Phelan, the Manchester United assistant manager, admitted afterwards that a furious Ferguson was 'not in a fit state' to speak to the media following Cakir's sending off of Nani.
"It speaks volumes that I am sat here," Phelan said, who said he had never seen a worse moment of injustice in football.
"We are all witnesses to a decision that seemed very harsh, and incredible at that moment in the game.
"To say we are disappointed is an understatement. We felt as though we had got things right tactically and were reasonably comfortable.
"That amazing decision changed things totally. Referees are there to make decisions in big games.
"There is an element of doing the right thing at the right moment. It is a disappointing one. It spoiled the game."
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