Ozil failed to come out for the second-half as Arsenal drew 1-1 at holders Bayern on Tuesday in the last 16, second-leg, as the Gunners bowed out 3-1 on aggregate.
Gunners manager Arsene Wenger said Ozil will definitely miss their English Premier League game at Tottenham Hotspur on Sunday.
"Ozil has a hamstring injury and it looks quite serious," said Wenger. "He will miss the Tottenham game for sure, he needs a scan. He's out for at least a few weeks."
The Munich injury caps a miserable two legs for ther German international, who failed to convert a crucial penalty in the 2-0 first-leg defeat in London and apologised to Gunners fans via Facebook.
He is one of Germany's key players, with Joachim Low's side set to launch their FIFA World Cup™ campaign against Portugal on 16 June.