Kevin Davies' late goal sealed an epic European result for struggling Bolton and boss Gary Megson in the Uefa Cup.
Davies helped Bolton pull off a surprise draw at Allianz Arena
Davies grabbed an unlikely draw for the visitors when he slipped the ball under keeper Oliver Kahn in the 82nd minute.
Bolton had earlier stunned the hosts with Ricardo Gardner's deflected shot eight minutes in.
But Lukas Podolski equalised for the Bundesliga leaders on the half-hour mark with a low drive before claiming his second just after the break.
Thursday's tie always promised to be a mountain to climb for Bolton, who are languishing at second-from-bottom in the Premiership.
While Megson side's have only mustered one league win so far this season, Bayern remain unbeaten in all competitions this season and sitting pretty on top of the Bundesliga with a goal difference of plus 23.
But the opening 10 minutes at Allianz Arena hinted that Megson's first taste of European football - and only fourth game in charge - might end in a surprise result.
The dream start came when Gardner bundled in a deflected shot off the crossbar, after Kevin Nolan's long throw caused chaos in the box, to score his first goal since Boxing Day 2002.
But Bayern soon upped their game with Podolski, Franck Ribery and Bastian Schweinsteiger terrorising the Bolton defence.
The three combined in an intricate passing move down the left, started by Podolski and ending with his low arched shot past inexperienced goalkeeper Ali Al Habsi.
The hosts continued to pile on the pressure with Schweinsteiger missing the best chance before the break, when his close-range shot went into the side netting.
But their patience was rewarded four minutes into the second half when Ribery ripped through the Bolton defence once again, squaring an easy lay-up on the right for Podolski to grab his second goal.
As the German barrage ensued, it looked as though Bayern's third was only a matter of moments away - perhaps leading manager Ottmar Hitzfeld into a false sense of security.
Hitzfeld, the only man to win the Champions League as coach of two different clubs, opted to take off two of his best players - Ribery and Schweinsteiger - as Bayern marched to victory.
But Bolton had other ideas as Davies pounced on Nolan's pass to the back post and lashed a shot under Kahn with just eight minutes left.
It was his first of the campaign and not a moment too soon as Bolton held on for a shock away draw.
Bolton boss Gary Megson:
"It was very encouraging - but then I've been hugely encouraged since day one, with the application.
"You've seen it tonight - they've stuck at it. We got away with it once or twice, but it was good.
"We keep drawing games. We had 12 players missing against a club of this stature, and it was terrific."
Bayern Munich: Kahn, Jansen, Lucio, Van Buyten, Lell, Ribery (Kroos 60), Ottl, Van Bommel, Schweinsteiger (Altintop 73), Podolski (Toni 57), Klose.
Subs Not Used: Rensing, Ze Roberto, Schlaudraff, Sosa.
Goals: Podolski 30, 49.
Bolton: Al Habsi, Andrew O'Brien, Cid, Michalik, Gardner, Alonso (Giannakopoulos 56), Nolan, Guthrie, McCann, Braaten (Teymourian 77), Davies.
Subs Not Used: Walker, Speed, Harsanyi, Sinclair, Sissons.
Booked: Davies, Braaten, Cid, Andrew O'Brien.
Goals: Gardner 8, Davies 82.
Ref: Jaroslav Jara (Czech Republic).