Trotters boss Gary Megson handed only a second start for the club to goalkeeper Ali Al Habsi, while Gerald Cid and Lubomir Michalik came in for the injured Abdoulaye Meite and Nicky Hunt.
Just eight minutes in Wanderers took a shock lead as Kevin Nolan's long throw-in caused chaos and Ricardo Gardner's shot was deflected up and over the stranded Oliver Kahn. Left-back Gardner had previously not scored since Boxing Day 2002, when he found the net in a 4-3 victory over Newcastle United.
Seventeen minutes in Andreas Ottl shot high over the crossbar after superb work on the right by Franck Ribery.
Just before the half-hour mark Bolton came close to doubling their surprise lead, as Davies shot inches wide after finding space on the edge of the area, but Bayern were level within a minute.
Lukas Podolski exchanged passes with Ribery and Bastian Schweinsteiger before firing a left-foot shot beyond the despairing dive of Al Habsi.
Shortly afterwards the keeper had to be alert to field another Ribery effort as Bayern turned up the heat and the France winger threatened again, nine minutes before the break, after cutting in from the left.
Schweinsteiger wasted a chance to give Bayern the lead a minute before the interval, shooting wide of an open goal after Al Habsi had blocked his initial shot.
Four minutes into the second half Bolton fell behind as Ribery again broke clear over on the right and his cutback was blasted home from close range by Germany forward Podolski.
On the hour Al Habsi made an astounding save to push Ribery's drive over the crossbar for a corner and the Bayern forward left the pitch to a standing ovation soon after.
Al Habsi tipped away a Schweinsteiger piledriver as the home side made all the running and Mark van Bommel's drive was deflected just wide 18 minutes from time.
However, battling Bolton stunned the home fans again eight minutes before the end as skipper Kevin Nolan forged an opening and Davies fired a low shot under Kahn from 12 yards to make the score 2-2.