Croatia striker Mario Mandzukic grabbed the opener, turning home Dutch international Arjen Robben's cross.
Bayern played the better football throughout with Franck Ribery and Arjen Robben hitting the woodwork.
Messi escaped the attentions of Arjen Robben, but was halted by a clumsy challenge by Chelsea's Spanish defender.
Giovanni van Bronckhorst, Wesley Sneijder and Arjen Robben each scored to earn a clash with Spain or Germany.
The experienced and consistent former Lyon star may provide a more reliable influence than the injury-plagued Arjen Robben.
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.
Add that to the absence of Arjen Robben and all of a sudden people are asking questions of them.
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Wigan have defender Arjen de Zeeuw back to lead their side after an ankle injury and Kevin Kilbane replaces Julius Aghahowa.
Fellow Dutch internationals Ruud van Nistelrooy, Arjen Robben and Wesley Sneijder have all been linked with moves away from the Bernabeu.
Real had been poor and Arjen Robben had their best chance when his shot was steered over by keeper Jose Reina.
Goals in each half from Andre Ooijer and Arjen Robben gave the Dutch their seventh straight win in the qualifying phase.
Cole's former team-mate Arjen Robben has even suggested that the combination of Torres, Gerrard and Cole is as good as Barcelona's attack.
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The impressive Arjen Robben was a constant threat and wasted several glorious openings while Lampard curled a free-kick narrowly over the bar.
Javi Martinez, Arjen Robben and Franck Ribery were also on the scoresheet.
Bayern Munich star Arjen Robben had a chance to level matters but he wasted a glorious chance, heading wide from a pinpoint Daley Blind cross.
The author of the report, Arjen Wals, UNESCO Chair of Social Learning and Sustainable Development at Wageningen University, The Netherlands, presented the publication.
Joe Cole looked one of the few players capable of livening things up before he was surprisingly replaced at half-time by Arjen Robben.
They suited 4-3-3 and they had their best seasons when they had Joe Cole on the right and Arjen Robben on the left.
BBC: SPORT | Football | Premier League | Alan Hansen's column
It's just as telling that Heynckes was able to leave two world-class internationals on the bench in Germany's Mario Gomez and the Netherlands' Arjen Robben.
The pair have been named on a 10-man shortlist for the Fifa Puskas Award, along with the likes of Arjen Robben and Arsenal's Samir Nasri.
"It shouldn't have been that close, " Bayern forward Arjen Robben said.
Wesley Sneijder restored the Dutch side's lead despite Robin van Persie appearing to be offside, and an Arjen Robben header made it 3-1 three minutes later.
"As a result, Holland were put in a situation that if Arjen Robben and Robin van Persie were not playing well, there was no alternative, " Cruyff said.
BBC: SPORT | Football | African | Cruyff regrets Kalou absence
Mikel Jon Obi, Arjen Robben and Wright-Phillips were struggling to get in the game and Norwich, with Etuhu and Darren Huckerby to the fore, were posing problems.
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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The home fans at the Ricoh Arena were in raptures, but West Ham were given a lifeline when Boa Morte pounced on Arjen de Zeeuw's weak clearing header.
Bayern trailed 1-0 from the first leg, but their Swiss visitors were overwhelmed in the Allianz Arena once Arjen Robben had scored the opener after just 10 minutes.
Chelsea's day got worse after 20 minutes, when Arjen Robben - who had twisted his ankle in an earlier challenge - limped off to be replaced by Shaun Wright-Phillips.
"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.
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