The 56th-minute red card, shown for a dangerous challenge, was the turning point of the game as Real won 2-1 on the night and 3-2 on aggregate with goals from Luka Modric and Ronaldo after United had gone ahead thanks to a Sergio Ramos own goal.
United manager Sir Alex Ferguson was so upset by Turkish referee Cuneyt Cakir's controversial decision that he sent assistant Mike Phelan to address a packed news conference.
"A great performance was marred by one decision," said Phelan. "Extremely disappointed, everyone wondering why it had happened, a distraught manager, that's why I'm sitting here."
Real coach Jose Mourinho had some sympathy for his opponents, saying that on another occasion it could have been a yellow card and United had actually been the better side.
"When you are talking about football at this level... playing with one man down for such a long time is going to have a big impact on the game," said the Portuguese.
"In my opinion, the best team lost."
All the talk before the last 16, second leg game had been about the return of former Old Trafford darling Ronaldo and when the teams were introduced the home fans gave the Portugal winger a rapturous ovation that carried on into the match.
That was, however, the noisiest it got for him in the first half as he was contained by an organised United side, with the likes of midfielder Ryan Giggs, making his 1,000th career appearance, helping defend almost as much as the back four.
In an enthralling first half, United went close to opening the scoring after 21 minutes when Nemanja Vidic thundered a powerful downward header against Diego Lopez's left-hand post, only to see the ball rebound to Danny Welbeck.
The England forward had little time to react but shot first time straight at the keeper sitting on the line, who smothered it between his legs. TV replays, however, showed Welbeck was in an offside position and the goal would not have counted.
United finally made the breakthrough three minutes into the second half after a good run by Rafael put Robin van Persie through.
The Dutchman's shot was blocked and Real defender Raphael Varane failed to clear, giving Nani the chance to drive a low ball into the area that Ramos poked into his own net after Welbeck's got a touch on the ball.
The momentum was with United but it was short-lived when eight minutes later a stunned Old Trafford crowd grappled with the sight of Cakir brandishing a red card at Nani.
The Portugal winger had inadvertently gone in high on Alvaro Arbeloa, with the defender lifting his shirt to demonstrate where he had been caught by a boot across the ribs.
Nani certainly had his foot up as he challenged for the ball with Arbeloa, but did not see the Spaniard behind him and had his eye on the ball throughout the incident.
With Ferguson gesturing to the home fans that they should raise the deci
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