The 26-year-old Germany international injured right ankle ligaments in training on Thursday afternoon after clashing with team mate Arjen Robben.
The Dutch winger is suspended for the game on Sunday after being sent off last week.
With five matches each to play, Bayern are fourth on 52 points, one behind third-placed Hanover 96, while Leverkusen have 61.
St Pauli will not play their next home game behind closed doors after the German federation reduced their sentence to playing their first home game next season in a neutral ground 50 kilometres or more away from their home city Hamburg.
The relegation-threatened club had been punished for violent fan behaviour in their game against Schalke earlier this month when the linesman was hit by a plastic beer cup and the game was stopped a minute from time.
Schalke, leading 2-0 at the time, were awarded the three points.
The federation said it did not want to influence the outcome of the current season.
The 22-year-old, who had been a key influence in their recent good form, will undergo surgery in his right ankle.
"He has torn his ligaments twice there and there was no stability. We tried it with a special shoe but it just got worse," coach Bruno Labbadia said.
The 2007 Bundesliga champions are far from safe, lying in 15th place on 30 points, two above the relegation play-off spot.