The Gunners, who trailed 2-0 from the first leg in north London last month, were beaten thanks to goals from Neymar, Luis Suarez and Lionel Messi, despite Mohamed Elneny netting his first goal for the club.
Flamini was substituted and replaced by Francis Coquelin on the stroke of half-time at Camp Nou after sustaining a problem.
And speaking after the game, Wenger confirmed that the midfielder had suffered an injury, but Arsenal did not yet know the extent of the problem.
Asked about Flamini in his post-match news conference, Wenger said: “He was injured. He had treatment, then after I don’t know.”
Speaking to BT Sport after the game, Wenger also confirmed that he brought Danny Welbeck off in the second half merely as a precaution as the striker finds his way back to full fitness after a lay-off with a knee injury.
Arsenal travel to Everton in the Premier League on Saturday lunchtime.
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