Ozil was withdrawn at half time of last night’s last 16 tie, after picking up a hamstring injury.
The German international has struggled to find his best form in recent weeks, but the news will still come as a big blow to Arsene Wenger’s title hopes.
Arsenal lost another midfielder only last week, when Jack Wilshere was ruled out for six weeks after injuring his foot while playing for England.
On the loss of Ozil, boss Arsene Wenger said: “It looks quite serious.
“I don’t know (how long he will be out for), but for sure he is out (of the Tottenham game on Sunday).
“We have to make a scan tomorrow to see how bad it is but he’s out for at least a few weeks. I hope it’s not too bad.”
Arsenal were only able to name six substitutes at the Allianz Arena last night, with Ryo Miyaichi travelling as part of the squad only to discover he was not eligible for the pre-submitted Champions League squad.
“He was not eligible because he was not qualified to play in the Champions League because I wanted to give him out on loan, so we took him out of the list and UEFA informed us today that he is not qualified,” Wenger added.
“Because he was on the bench on Saturday (against Everton), naturally he was with us but honestly that did not have an impact on tonight’s result.”