He was limping badly after pulling a calf muscle while running for apass in the 86th minute of a defeat that has also damaged Bayern'shopes of the Bundesliga title.
The Holland winger spent the remaining few minutes standingforlornly on the touchline after his appeals to come off were met withdeaf ears by hard-line manager Louis van Gaal, who had already used histhree substitutions.
Injury doubt: Bayery Munich's Arjen Robben may miss the Champions League match against Manchester United
A concerned Van Gaal said: 'We don't know how bad it is - the doctor needs to have a proper look but we hope it may just be a tightening of the muscle. Certainly, Robben is a hard player for us to replace so we will be crossing our fingers.'
The in-form Robben had started on the bench alongside Bayern's other star player, Franck Ribery, in order to rest for the United game but both men were sent on at half-time as Van Gaal's side struggled.
Sir Alex Ferguson's spies will have seen this Bayern team are much better going forward than they are at the back. Ivica Olic put them ahead after 31 minutes but they were then undone by goals by Christian Trasch and Ciprian Marica.
Van Gaal now has big problems ahead of the United game. Besides ex-Chelsea winger Robben, midfielder Bastian Schweinsteiger is suspended and first-choice striker Mario Gomez will be fit enough only to be on the bench, giving a rare starting chance for Miroslav Klose.
Van Gaal is under pressure to deliver a trophy this season after introducing so many strict rules that he makes Ferguson look like a floppy liberal.
Robben, Ribery and the other stars live under a regime designed to restore order to a club dubbed 'FC Hollywood' after years of in-fighting and lack of discipline.
Players are told how to dress and where to sit on the team coach, and toilet breaks are banned at half-time while Van Gaal is issuing his orders.
Danger man: Arjen Robben in action for Bayern Munich against Stuttgart
The whole squad not only eat together but Van Gaal insists everyone on the table rises at the same time to collect their food.
Only when they have sat down with their filled plates, can the next table get up in unison.
Van Gaal's rule of iron has seen him fall out with Ribery, whom he refused to put straight back in the team following a knee injury.
He has also alienated the board with of his scant use of Anatoliy Tymoschuk. Defender Philipp Lahm says Bayern have a much better chance against United under Van Gaal than former boss Jurgen Klinsmann, however.
Lahm said: 'We are much better prepared than in the past. We know what to do. There are clubs with better players, like United, Barcelona and Inter Milan. But, as a team, we can be the dark horses.'
'United are favourites. Wayne Rooney seems to score every time he gets a chance. We will have to mark him close, be very tight.'
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