The German suffered condemnation from certain sections of the media for his performance in the Allianz Arena before he was substituted at half-time.
Ozil has now explained his muted performance on his Facebook page.
He writes: 'Dear friends, now it's clear: during the #ucl match against #FCBayern I suffered a muscle injury in the second minute. I tried to give my best and played until the end of the first half. Rest assured that I'll be back even stronger!'
Speaking ahead of Sunday's north London derby with Tottenham, manager Arsene Wenger told arsenal.com: "He's out. I don't know for how long but it is a hamstring injury. There are scans going on."