The 29-year-old was forced off after 20 minutes as United came back from a goal down to beat the German champions 2-1 at Old Trafford.
"Groin injuries are difficult to say. He could be out two or three weeks," said United boss Alex Ferguson after the game.
"His fitness levels are good so we shouldn't need to worry too much about it. We will treat it as a normal groin injury.
"He felt his groin after training on Sunday and he trained a little bit on Monday but had a rest day on Tuesday and he thought he was fine."
Owen was hoping to join the England squad travelling to Ukraine on October 10th for a World Cup qualifier, but the injury puts his return to the Three Lions beyond doubt.
Giggs Praise
While he was left to bemoan the injury of one player, Ferguson hailed the contribution of veteran Ryan Giggs, who scored one and set up another goal on Wednesday.
"The amazing thing about Ryan is the incredible youthfulness about his performances," said Ferguson.
"It's as if he is just starting his career. He is continuing like a young man enjoying his football and it's wonderful to see."