The contest was effectively over at half-time as Bayern led by two goals and had also struck woodwork twice and it was a case of attempting damage limitation for the Dons in the second half.
The Germans hardly let up and the only crumb of comfort for Aberdeen was a late consolation goal.
Bayern started impressively with Luca Toni chesting the ball into the path of Lukas Podolski and his left-foot shot crashed against the crossbar with Jamie Langfield well beaten.
It was one-way traffic from the start and Langfield had to get down smartly to smother another effort from the dangerous Podolski.
Bayern took the lead in the 12th minute after Alan Maybury gave away a free-kick at the edge of the area. Brazilian Lucio cracked the ball over the wall and past a bemused Langfield into the net for the early breakthrough they wanted.
Langfield did well to save from Hamit Altintop after Podolski had set up the chance as Aberdeen struggled to cope with the Germans.
Darren Mackie had a rare chance for Aberdeen after a long through ball but he dragged his shot wide of goal midway through the first half.
But Bayern hit back and Langfield had to block a shot from Toni and send it past for a corner with Aberdeen stretched at the back.
Andreas Ottl tested the Aberdeen goalkeeper again but it was straight at Langfield and he dealt with it comfortably.
It was 2-0 after 36 minutes when Belgian defender Daniel Van Buyten outjumped the Dons defence to head home a free-kick from Toni Kroos.
Aberdeen almost lost a third on the stroke of half-time after Langfield parried an Ottl shot and Lucio's follow-up shot struck the post.
Darren Mackie had the ball in the net for Aberdeen after 56 minutes but the effort was disallowed for offside against Lee Miller.
Bayern had another chance and it was Mark van Bommel who tested Langfield again after another sweeping move overwhelmed Aberdeen.
Podolski added the third after 71 minutes when Langfield was unsighted in a crowded area and the German cracked it high into the net.
It was 4-0 six minutes later when Podolski headed down a corner from Bayern substitute Bastian Schweinsteiger.
It took Aberdeen 82 minutes to get a shot on target, but Oliver Kahn pulled off a wonderful save to deny Barry Nicholson. But substitute Steve Lovell scored a consolation a minute later when he produced a fine header from a Jeffrey De Visscher free-kick.
Bayern finished in style with van Bommel netting the first with a superb strike after another sweeping move.