The home side was left seething with injustice as it crashed out of the competition.
A night that began with the shock of Wayne Rooney's omission and Ryan's Giggs starting in his 1000th professional game, ended in bitter frustration and recrimination as goals from Luka Modric and Ronaldo secured a 3-2 aggregate success for Madrid.
It was the controversial dismissal of Nani for a second-half foul on Alvaro Arbeloa that was the talking point.
At the time, United was leading through Sergio Ramos' own-goal and 2-1 up in the tie.
The pivotal decision of Turkish referee Cuneyt Cakir turned all those hopes to dust, left Rio Ferdinand applauding sarcastically after it was all over and Jose Mourinho celebrating, the former Chelsea boss offering a fuming Sir Alex Ferguson a consoling pat before heading down the tunnel before the final whistle.
"The manager is not in fit state to talk to the referee about the decision," United assistant coach Mike Phelan said of Ferguson.
"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."
Mourinho's comments that his side was second best on the night will not help Ferguson's mood.
"Independent of the decision, the best team lost. We didn't play well, we didn't deserve to win but football is like this," the Portuguese told ITV1.
"I'm not speaking about the decision because I'm not sure about it."
When pressed further, Mourinho quickly added: "But independent of that the best team lost."
The bombshell of Rooney's omission and an ovation for Ronaldo as loud and as long as any home player has received this season set the scene for a match Mourinho said yesterday the "whole world would be watching".
Those who did would have been enthralled by a frenetic contest, largely played in midfield, which justified Ferguson's shock selection.
At 39, Giggs was not the obvious choice to shackle Ronaldo.
But the Welshman did a magnificent job.
And he was not restricted to defensive duties either. Though opportunities for both sides were limited, Giggs did find time to get forward, delivering one brilliant cross for Robin van Persie, whose attempt to finish was blocked by Sergio Ramos.
If Giggs excelled, Danny Welbeck was the biggest threat, just as he had been in the first-leg.
His running from deep positions caused Real a problem, especially out wide.
It was Welbeck who provided that crossing opportunity for Giggs, having earlier presented Nani with a similar chance, which Fabio Coentrao flicked away before the veteran Welshman could pounce.
The one flaw in Welbeck's game is a lack of goals.
His effort in Spain was one of only two this season, and twice he wasted more openings to break the deadlock.
The first came after Nemanja Vidic soared to meet Van Persie's
corner, only for his thundering header to cannon back off a post,
straight to Welbeck, who prodded the rebound straight at Diego Lopez - although he was called for off-side to spare his blushes.
Welbeck's second chance was also on the rebound, after Lopez had parried an instinctive effort from Van Persie.
The England man should have made Lopez work. Instead he drove his shot into the ground, which allowed the visitors' keeper to save easily.
Real had even fewer sights of United's net.
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 as Kaka came on and which Real was still adjusting to when United struck on 48 minutes.
Rafael's surge to the edge of the box had Real floundering and although 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.
It all looked to be going to so well.
And then the roof caved in.
When Nani challenged Arbeloa for a bouncing ball inside his own half, he seemed committed and nothing more.
Cakir deemed his foot high and dangerous and after waiting until the winger recovered from a non-existent injury, out came the red card.
Nani was incredulous. Ferguson went ballistic.
And with good reason. Repelling Real with 11 men had been tough, with 10 it was bordering on the impossible.
Though it hung on grimly, with Rafael seeming to keep a goalbound Higuain header out with his arm, it took the visitor just 10 minutes to turn the entire tie on its head.
Modric struck first, with a viciously curling effort from 25 yards that went in off the post.
Three minutes later Mesut Ozil found Higuain, with a neat back heel, whose cross was turned home at the far post by the man United must have known would score.
At times like those, the money pocketed for Ronaldo is scant consolation, particularly as his enduring affection was seen in a refusal to celebrate.
The hopeless search for goals forced the 10-men down to the other end.
Rooney, by now a potential saviour, had a chance that he volleyed over the bar from six yards.
With that shot sailed United's European hopes.