Owen, 29, had been hoping for a recall to Fabio Capello's England squad for the World Cup qualifiers against Ukraine and Belarus next month.
The striker picked up a groin injury over the weekend but had declared himself fit for the game against Wolfsburg but he was forced off after just 20 minutes.
"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," United manager Alex Ferguson said.
"But groins are groins and on a wet surface he turned quickly and it's gone again so we had to take him off.
"It's not a serious one but groin injuries can be troublesome and maybe two to three weeks. The only good part of it is his fitness levels are very good so he shouldn't need to worry too much about that."