From a position of some promise, 2-1 up on aggregate after Sergio Ramos' own goal, 10-man United were dumped out of the Champions League as Luka Modric and Cristiano Ronaldo scored to take Real Madrid into the quarter-finals.
United were seething at referee Cuneyt Cakir's decision to red card Nani for a high tackle on Arvelo Arbeloa.
Rio Ferdinand applauded the official sarcastically after the final whistle, whilst a clearly incensed Ferguson took the unprecedented step of avoiding media duties, presumably for fear of what he might say.
"The manager is not in fit state to talk to the referee about the decision," said United assistant manager Mike Phelan.
"It speaks volumes that I am sat here.
"We are all witnesses to a decision that seemed very harsh, and incredible at that moment in the game."
In his role as pundit for ITV, former United skipper Roy Keane claimed the decision to dismiss Nani had been correct.
It was not a view shared by many. And none in the dressing room he inhabited for so long.
"To say we are disappointed is an understatement," said Phelan.
"We felt as though we had got things right tactically and were reasonably comfortable. That amazing decision changed things totally."
"Off the top of my head, no," added Phelan, when asked if he had ever felt a greater sense of injustice.
"Referees are there to make decisions in big games. There is an element of doing the right thing at the right moment.
"All you guys and TV audience will have a decision. It is a disappointing one. It spoiled the game."
United did have chances in the latter stages, with skipper Nemanja Vidic going close, and also Michael Carrick.
But perhaps the best opportunity fell to Wayne Rooney, who had been controversially omitted from United's starting line-up.
Rooney's wife Coleen expressed her surprise prior to kick-off, and now there is sure to be speculation about the striker's United future.
However, with Ryan Giggs and Danny Welbeck - the most obvious men to profit from Ferguson's bold call - excelling, the decision was justified.
Even so, both camps had their take on the situation.
"The decision was tactical," said Phelan.
"In that dressing room, everyone was fit. But big decisions have to be made. Tonight we had the balance just right."
Typically, Mourinho was more forthright.
"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 (reporter) are nobody to put a question like that. I am nobody.
"He did a great job."