Injuries added to insult for Bayern
Midfield star Michael Ballack limped from the pitch in the second half after badly twisting his right ankle in a challenge.
He will be examined in Munich on the club's return, but coach Ottmar Hitzfeld fears the worst for the crucial Bundesliga clash at Weser Stadion.
"I don't know how long he will be missing," he told Bayern's official website.
Meanwhile, Paraguayan striker Roque Santa Cruz, whose equaliser against Deportivo briefly gave Bayern hope of saving their European season, left the pitch with a broken bone in his hand.
The South American will be examined by club doctors on Wednesday but has no chance of playing against Werder.
Left back Michael Tarnat was also forced to hobble out of the Champions League game with a dead leg and Hasan Salihamidzic failed to show for the second half after suffering from muscular problems.
The long injury list will increase the pressure on the German giants as they desperately look to salvage something from a disastrous week by taking three points against Werder.
