There is near universal agreement that United were playing superbly and on course for victory until Nani's contentious red card.
Here is a round-up of what the country's top football journalist said about the match.
Daily Telegraph: Devastated
Henry Winter: When Manchester United's devastated players finally emerged from the dressing room, they would not, probably could not talk. The club had advised them to stay silent over Cuneyt Cakir’s unspeakable decision to send off Nani. Their inner fury, the anger in the eyes said it all. United’s players felt the victims of grand larceny. It was impossible not to sympathise. A 36-year-old insurance agent from Istanbul knocked United out of Europe. Too many officials are too easily castigated in the modern era that is long on scrutiny and short on patience yet Cakir needs calling to account.
The Times: Raging Ferguson lost for words
Oliver Kay: Long before Ronaldo, with a stroke of his right foot, converted Gonzalo Higuaín’s cross to complete a four-minute turnaround in the tie, United’s players and supporters were seething with an anger the Real Madrid No 7 can hardly have recognised. Such was their sense of injustice over the decision by Cüneyt Çakir, the Turkish referee, to dismiss Nani for raising his right foot in a challenge with Álvaro Arbeloa in the 56th minute. In the end, this was not about Ronaldo. It was not even about José Mourinho or about Sir Alex Ferguson’s decision to drop Wayne Rooney from the starting line-up for the biggest game of the season. Çakir made dubious decisions at both ends of the pitch, but, as the game went on, he seemed to lose control — not to the same extent as Tom Henning Ovrebo, who infuriated Chelsea in a Champions League semi-final, second leg against Barcelona in 2009, but he was getting there.
The Guardian: Ronaldo deals the killer blow after Nani red card destroys United's hopes
Daniel Taylor: It was a night, ultimately, that will go in high on the list of Sir Alex Ferguson's more harrowing moments as Manchester United's manager. His players gave everything to overcome José Mourinho's team and will always be convinced that a night of incredible volume and high drama could have led them to glory rather than the crushing inevitability of Cristiano Ronaldo inflicting the final blow…The night was always going to be laced with controversy from the moment Cakir showed Nani a red card for embedding his studs into Alvaro Arbeloa's midriff as he went to control a high ball. Ferguson, in his 26 years at the club, has never before delegated a member of staff to face the media in these circumstances but the manager could not bring himself to attend the post-match conference. Mike Phelan described him as distraught and in "no fit state" to address what had happened. "It speaks volumes I am sat here," the assistant manager said.
Independent: United's huge resource of spirit undone by referee's terrible assault on game's natural order
James Lawton: Sometimes you cannot control your own fate. Sometimes it is taken away from you. So what can you do? If you are a football team filled with the most remarkable competitive instincts, you do what Sir Alex Ferguson's Manchester United did tonight. You fight Real Madrid with all your resources of spirit while lesser teams would collapse under the weight of their belief that the red card delivered to Nani, a potential match-winner, was a terrible assault on natural justice. United are out of Europe and immersed in controversy, some of their own making in the matter of the dropping of Wayne Rooney, but where they remain is among the most durable fighters in all of football. Even Jose Mourinho admitted the best team lost.
The Sun: Shattered
Steven Howard: And so, for the first time since 1995-96, there will be no English clubs in the quarter-final draw. Sole survivors Arsenal are 3-1 down against brilliant Bayern Munich and seemingly facing mission impossible in the Allianz Arena next week. But don’t blame United for that after suffering their first defeat of 2013. You can blame Manchester City, Chelsea and the Gunners. But what happened here last night had little to do with any shortcomings on behalf of a side that had made Real look second best for so long. With 11 men on the pitch, they had the game firmly in their grasp. They then gave it everything they had when reduced to 10 men and up against a team who had scored 27 times in 15 Champions League away games under Mourinho, never failing to find the net.
The Mirror: Wronged
Oliver Holt: In the biggest match at Old Trafford for five years, there was no Wayne Rooney… But let’s make one thing clear: Ferguson got his selection absolutely right on the night. United played superbly. Danny Welbeck stood out. Nani, Rooney’s replacement, created United’s goal. If Nani had not been sent off, United probably would have won. Ferguson’s tactics were irreproachable. Ferguson himself played down the decision to leave out Rooney and suggested he was lacking match sharpness. But there have been rumours for some time that the United boss has been falling out of love with Rooney.
Daily Mail: Robbed
Martin Samuel: It was rotten luck. It was highly debatable. And it will have been picked over until last orders or lights out at every bar, club and sitting room in Britain. Yet the bottom line is this: just because your fancy-dan winger gets sent off, whether rightly or not, it does not mean you have to concede two goals in the next 12 minutes and lose the tie. Manchester United were not forced to play without a central defender or goalkeeper. Nani has never been considered so vital to any defensive effort that his absence should have sent his team into a loop… Chelsea lost John Terry at the Nou Camp last season while 1-0 down. They did not lose the match that night, or the tie.
Daily Star: Red 'N Buried
Jeremy Cross: Life at Manchester United has come full circle for Wayne Rooney as his Old Trafford future looks in danger of spinning out of control. It was in 2010 that Rooney declared United were not good enough for him as he refused to sign a contract and threatened to leave. He changed his mind in the end, of course, but less than three years later it is crystal clear Rooney is not good enough for United. What other conclusion can be dawn from Sir Alex Ferguson’s bombshell decision to axe him from last night’s clash with Real Madrid?