The Bavarians, who had enjoyed a successful run in three competitions following the winter break, are stuck in a rut after their second successive Bundesliga loss, 2-1 to VfB Stuttgart on Saturday.
They could also take on United, 11 years after losing the 1999 Champions League final 2-1 when the English team scored two goals in the dying minutes, without their best player this season.
Dutch winger Arjen Robben pulled a calf muscle against Stuttgart and is doubtful for the match while midfielder Bastian Schweinsteiger is suspended.
"Maybe it turns out not to be that bad but it looks difficult for the match against Manchester," Bayern coach Louis van Gaal told reporters.
Robben was also outstanding in midweek, scoring the extra-time winner against Schalke 04 which sent Bayern into the German Cup final.
"It would be extremely bitter if he is missing from such a top game," said Bayern defender Philipp Lahm.
Van Gaal, however, does have playmaker Franck Ribery fit as well as central defender Martin Demichelis, who injured his face in Argentina's friendly against Germany this month.
Striker Mario Gomez also looks to have recovered from a muscle injury, though he lacks match practice.
WINNING STREAK
United have no new injury concerns with top scorer Wayne Rooney and defender Rio Ferdinand likely to be fit after being rested from Saturday's 4-0 victory over Bolton Wanderers, their seventh straight win in all competitions.
With a huge Premier League game against Chelsea next Saturday, it was no surprise that Alex Ferguson opted to rest to duo.
He said Rooney, who has scored 33 goals this season, was left out because of a bruised foot while Ferdinand has struggled with a back problem and picked up a groin strain in training.
"They were just a bit tender," Ferguson told MUTV. "Wayne's got a bruise on his foot. If he'd played and got a whack on it, then he would have been doubtful for Tuesday.
"We've got a big week. We have to use our squad in situations like this. I've no qualms about that at all. They've all done their job well and I'll have Rooney and Ferdinand available for Tuesday."
Ferguson, seeking to lead United to their third Champions League final in a row, will also be delighted with Dimitar Berbatov's form.
The Bulgarian striker, yet to convince many United fans of his worth, scored twice against Bolton and seemed to revel in the responsibility of leading the line on his own.
Portuguese winger Nani, enjoying his best season, was another on top form and Bayern will have to work hard to prevent him and Antonio Valencia from delivering the crosses that Rooney, in particular, has been thriving on. Probable teams:
Bayern Munich: 22-Hans-Joerg Butt, 5-Daniel van Buyten, 6-Martin Demichelis, 21-Philipp Lahm, 28-Holger Badstuber; 7-Franck Ribery, 17-Mark van Bommel, 25-Thomas Mueller, 23-Danijel Pranjic; 18-Miroslav Klose, 11-Ivica Olic.
Manchester United:
