Bayern played the better football throughout with Franck Ribery and Arjen Robben hitting the woodwork.
But Weidenfeller couldn't do much in the 60th minute after Franck Ribery clipped a ball through three Dortmund defenders.
Bayern Munich's goal-scoring duo of Arjen Robben and Franck Ribery (known as Robbery) can make defenders dizzy as well.
Bayern had taken the lead before half-time, Arjen Robben slotting in from the spot after Franck Ribery was fouled.
Gomez couldn't apply the finishing touch to Franck Ribery's shot across goal and then blasted over from a promising position.
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Winger Franck Ribery scored the game's only goal from the spot after Henry was fouled in the box on 24 minutes.
Despite the vast outgoings, Real have also been linked with Liverpool's Xabi Alonso, Valencia's David Villa and Bayern Munich's Franck Ribery.
Javi Martinez, Arjen Robben and Franck Ribery were also on the scoresheet.
United have been linked with moves to sign Bayern Munich's France star Franck Ribery and Wigan's Ecuador winger Antonio Valencia as Ferguson seeks to replace Ronaldo.
Most of the French squad are black, and many are Muslim, including Mr Anelka, who is a convert to Islam, as is Franck Ribery, who is white.
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Among those to be linked with a move to the Premier League champions are Brazilian forward Douglas Costa, French playmaker Franck Ribery, and Spain striker David Villa.
Bayern, missing the suspended Franck Ribery and with Arjen Robben only an intermittent threat, had a golden chance to equalize in the opening attack of the second half.
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Real are reported to be lining up further big-money moves, with Bayern Munich winger Franck Ribery and Liverpool midfielder Xabi Alonso said to be on their wanted list.
Franck Ribery set up the further goals, first bursting clear down the left in the 72nd minute to see his cross turned clumsily into his own net by Pique.
The best chance of the half fell to Anelka, who reacted quickest to a left-wing cross from Franck Ribery but could only loop a weak header over the crossbar.
German giants Bayern Munich plan big wage cuts, according to Britain's Guardian newspaper, and may be forced to sell star asset Franck Ribery, long a target of Real, United and Chelsea.
"Robbery, " as Arjen Robben and Franck Ribery are jointly known, are the speedy wingers who have dazzled the soccer world and led Bayern to its second Champions final in three seasons.
Bayern coach Louis van Gaal replaced Gomez with Franck Ribery in the second half, and the Frenchman was involved as Bastian Schweinsteiger made it 2-1 with a low shot from outside the area.
Florent Malouda's searching run allowed Franck Ribery to tee-up Nasri for a clinical strike from the edge of the penalty area that flew past his City team-mate, Joe Hart, six minutes before half-time.
United have been linked with Lyon striker Karim Benzema, who is set to join Real, while Bayern Munich forward Franck Ribery has been linked with a move to the Madrid club rather than the English champions.
In extra time it was France who looked the more likely to score as Franck Ribery shot agonisingly just wide after 99 minutes before Zidane forced the spectacular save from Buffon after meeting a Willy Sagnol cross with a stunning header.
Franck Ribery was an early threat down the left and his low cross after seven minutes should have been converted by Govou, while playmaker Yoann Gourcuff had few opportunities to showcase his skills - although he almost caught Fernando Muslera out with a free-kick from a tight angle on 17 minutes.
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