Martin Demichelis' latest match-winning goal separated the sides as Bayern dominated on the first big European night at the Allianz Arena.
Another 66,000 capacity crowd saw the home side boss the first half against the ultra-defensive Belgians but fail to create much in the way of clear-cut chances.
Demichelis broke the deadlock on 32 minutes, bludgeoning the ball into the roof of the net after Bruges keeper Tomislav Butina flapped at a corner, but the Reds had nothing more to show for their superiority at the break.
Top two claim maximum points
Bayern continued to control possession in the second period but the German champions were a long way below their imperious best and finished the match content simply to bring home the points.
With Juventus defeating Rapid Vienna 3-0, the two favourites in Group A both have maximum points to set up a mouth-watering double encounter next month.
Felix Magath made two changes to the side which lost in Hamburg at the weekend, selecting Bastian Schweinsteiger wide on the right in place of Hasan Salihamidzic, and restoring Paolo Guerrero to a two-man forward line in place of Ali Karimi, sidelined with a throat infection.
Micho applies decisive touch
The sides traded early half-chances, Demichelis heading over and Bosko Balaban coming within inches of connecting with a diagonal ball across the face of Oliver Kahn's goal, before the home side assumed almost total control.
Veteran campaigner Bixente Lizarazu was buzzing with intent, bursting down the inside left channel to shoot goalwards on three occasions and almost scoring on 26 minutes when Birger Maertens deflected narrowly past the upright.
Michael Ballack had earlier curled a free-kick just inches wide and Kahn had acrobatically headed clear with Balaban lurking, before Demichelis reacted first to the loose ball after Butina's woeful misjudgement, crashing home from close range to open the scoring with 32 minutes played.
Scholl's immediate impact
The Reds were content to protect their lead until the break but the pattern was the same after the restart as Ballack drove a 49th minute half-volley spectacularly but inaccurately over the bar.
There was a score for Bayern when Ivan Leko flashed a drive across goal before Lizarazu pulled up with all the hallmarks of a torn muscle and was replaced by another stalwart, Mehmet Scholl.
The former Germany international wasted no time stamping his elegant presence on the game, unleashing a stunning 25-metre free-kick only for Butina to redeem himself with a excellent stop.
Ballack and Scholl both came close before Roque Santa Cruz replaced the tiring Guerrero after 72 minutes. Demichelis might have sealed the points just a minute later, but the Argentine's header from Willy Sagnol's floated free-kick drifted over the bar.
Ballack limps off ten minutes from time
Bayern's single-goal lead began to look fragile as Bruges finally threw caution to the wind in the last quarter of an hour, but young Jason Vandelannoite missed a golden opportunity to equalise.
Zé Roberto, lively but still a shade below his best, set up a superb chance on the break with ten minutes remaining, but the subdued Roy Makaay could not convert.
The Reds' efforts to repel the onslaught in the closing phase suffered a blow when Ballack limped off, but experience was to hand in the shape of sub Jens Jeremies.
The German double winners did what was necessary to preserve a second 1-0 victory in this term's Champions League, and will certainly point to the fact the result counts more than the manner in which it was achieved.
| Bayern Munich - Club Bruges 1-0 (H-T: 1-0) | |
| Bayern Munich | Kahn - Sagnol, Lucio, Ismael, Lizarazu (Scholl 52) - Demichelis - Schweinsteiger, Ballack (Jeremies 83), Zé Roberto - Makaay, Guerrero (Santa Cruz 72) |
| Club Bruges | Butina - de Cock, Maertens, Van Delannoite - Dufer, Englebert (Roelandts 85), Vermant, Blondel - Verheyen (Yulu Matondo 75), Balaban, Leko (Portillo 68) |
| Referee: | Tom Henning Övrebö (Norway) |
| Spectators: | 66,000 (capacity) |
| Goals: | 1-0 Demichelis (32) |
| Yellow Cards: | Ballack, Sagnol / Vermant, Van Delannoite |