The versatile 22-year-old was substituted at half-time at the Ernst Happel Stadium, after hurting his left knee in a challenge with Hoffenheim's Ermin Bicakcic.
Alaba spent more than two months on the sidelines earlier this season after partially tearing the medial ligament and damaging the meniscus in his right knee during Bayern's 2-0 win over Roma in the group stages of the UEFA Champions League.
And he could now be set for another lengthy lay-off as he awaits a diagnosis of his latest injury.
Kronen Zeitung quote Alaba as saying: "I have very, very strong pain. [I] can barely walk. I really do not know what's going on."
Bayern, who remain in the hunt for three trophies this term, face Borussia Dortmund in the Bundesliga on Saturday.
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