Alaba went down to the turf holding his left ankle following a challenge with Georgia midfielder Valeri Qazaishvili at the Ernst-Happel Stadion, and it soon became clear he would be unable to continue.
Austria were trailing to Valerian Gvilia’s early goal at that stage but Alaba’s replacement, Rapid Wien attacking midfielder Louis Schaub, smashed home an equaliser from close range before half-time.
That would be the end of the scoring, as Austria suffered a damaging 1-1 home draw against Georgia.
Bayern won the first two games of their Bundesliga title defence against Bayer Leverkusen and Werder Bremen, with Alaba playing every minute.
FCB evens to beat Hoffenheim -1 handicap
Carlo Ancelotti’s men are back in action at Hoffenheim on Saturday and begin their Champions League campaign when Anderlecht visit the Allianz Arena next Tuesday.