The Germany international could be out of action for a number of weeks due to a muscular problem, while Luiz Gustavo has also picked up a knock
The Germany international featured from the start in Sunday's encounter, but was forced to stay behind in the dressing-room at half-time due to a muscular problem.
Badstuber has yet to undergo further examination in order to determine the exact extent of the knock, but Heynckes fears the defender could face a spell on the sidelines.
"Holger has picked up a muscle injury. It's either a sprain or a muscle tear," the Bayern boss revealed.
Meanwhile, Luiz Gustavo also left the pitch in the second-half after picking up a knock and though his problem does not appear to be serious, he is a doubt for Wednesday's DFB-Pokal clash with Kaiserslautern.