The Armenia international started the first leg of the quarter-final tie but had to be substituted midway through the second half after picking up a knock.
Wenger has revealed that Mkhitaryan underwent a scan on Friday and the Arsenal medical team are still trying to determine exactly how serious the injury is.
However, the Arsenal boss confirmed that the 29-year-old would definitely be missing for Arsenal’s home clash against Southampton in the Premier League on Sunday afternoon.
Speaking in an interview with Arsenal Player, Wenger said: “Micki came off and he will be out for Sunday.
“He has a scan and the fear is that his medial knee ligament has been touched. We’ll know more about that soon. For how long he will be out, I don’t know.”
Arsenal are currently in sixth place in the Premier League table and looking as if they will have to settle for a spot outside of the top four for the second season running.
The Gunners’ best hope of securing a place in next season’s Champions League will be to win the Europa League this term.
Wenger’s men will travel to Russia for the return leg of their Champions League quarter-final tie on Thursday night against CSKA Moscow after having claimed a dominant 4-1 win in the first leg at The Emirates last week.
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