The 25-year-old Scotland captain, who had an outstanding match until his 75th minute sending-off, was adjudged by Italian referee Roberto Rosetti to have brought down Arsenal's Cesc Fabregas and denied him a scoring opportunity.
TV replays showed he clearly played the ball before impeding the Spanish midfielder.
Rosetti, though, showed him an immediate red card and awarded Arsenal a penalty which produced little more than a consolation goal for the dispirited home team who were 3-0 down on the night and 4-0 behind on aggregate.
Robin van Persie duly scored with the spot-kick but the sending-off, which cannot be appealed by the club, marred an otherwise perfect evening for United.
It also evoked memories of the bans imposed on Roy Keane and Paul Scholes who missed the 1999 Champions League final against Bayern Munich after picking up yellow cards in United's semi-final second leg against Juventus.
DIFFERENT DIRECTION
Manchester United manager Alex Ferguson said Fletcher was upset by the decision.
"He is very disappointed, he should be disappointed... he is one of the most honest players in the game and it's a tragedy for him that he will miss the final," Ferguson told reporters.
"You can see the ball has moved in a different direction. It's terribly unlucky and we can't appeal it. The referee is one of the best in Europe, he may look at it and have a view on it but there's nothing you can do about it."
Arsenal manager Arsene Wenger was also sympathetic.
"I have sympathy for Fletcher because I thought the sending-off was harsh," he said.
Former England manager Graham Taylor, commenting for BBC Radio Five Live, said: "It's taken something away from the game, that red card. You feel for people like Fletcher. He's a first-class pro."
Unlike the English Premier League which does allow appeals against dismissals, UEFA, European soccer's governing body, rarely overturns referee's decisions and Fletcher will certainly miss the final unless Rosetti admits he made a mistake.
Even then, UEFA is unlikely to grant him a reprieve.
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