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But the Dons will feel that they were cheated out of a memorable victory by a controversial second-half penalty award which handed Bayern an equaliser.
The teams were met by a wall of noise as they took to the field in front of a capacity crowd and the Dons made a lively start to the match against their star-studded Bundesliga opponents.
But it was the German giants who made the first clear opportunity of the match. Christian Lell let fly with a powerful 30-yard effort that was well touched behind by keeper Jamie Langfield, who dived full length to his right to make the save.
Aberdeen were closing Bayern down all over the pitch and their high tempo tactics paid off as the Pittodrie outfit took the lead midway through the first half.
Loan signings Sone Aluko and Josh Walker combined as Jimmy Calderwood's men made the breakthrough. Aluko brought the ball down in the box before laying off to Walker, who struck a sweet curling right-foot effort into the bottom corner of the net from 25 yards.
But the Dons lead was short-lived as Bayern levelled within minutes. A long ball down the middle from Lucio was flicked on by Luca Toni and Miroslav Klose got in front of Zander Diamond to smash the ball past Langfield.
Langfield had to be alert to stop Klose giving Bayern the lead seconds later as he made a fine point-blank save to deny the German sharp-shooter.
Having provided the assist for the opening goal, Aluko restored the Dons' lead with a stunning individual finish after 41 minutes. Lee Miller touched the ball on to Aluko, who took the ball past Lell with a sublime first touch before rifling the ball home from 16 yards.
Aluko almost made it two goals in the space of 90 seconds just before the break, but his 25-yard right-foot effort whistled inches wide of target.
A controversial decision from Spanish referee Eduardo Gonzalez saw the Germans draw level at the start of the second half.
The referee pointed to the spot after adjudging that Alan Maybury had intentionally handled the ball inside the area.
Hamit Altintop saw his spot-kick saved by Langfield, but the midfielder followed up to net the rebound, much to the consternation of the Pittodrie crowd who were clearly incensed at the controversial penalty award.
Bayern almost snatched a last-gasp winner, but Langfield did well to come off his line and dive at the feet of Toni as the Italian was set to shoot.