Bayern further extended their aggregate lead to 6-0 thanks to Thiago's well-taken 18th-minute strike, but the Spaniard had to come off 15 minutes later.
After netting his second goal in six Champions League games in this season's competition, a strong challenge from Erkin saw him limp off with James Rodriguez coming on as a replacement.
Having returned to action in February, putting a three-month absence behind him, Thiago suffers yet another injury blow.