Alaba scored the third goal in Bayern's 3-1 win at Signal Iduna Park, a result that moved them four points clear at the top of the Bundesliga.
However, his performance came at a cost, the full-back withdrawn in the 74th minute.
Further tests have revealed a muscle injury and the Austrian Football Association confirmed he would not feature in next week's clash with Uruguay in Vienna.
Bayern will hope the injury does not keep him out of their next league encounter, which comes against Bavarian rivals Augsburg on November 18.
Meanwhile, there was some good news for Jupp Heynckes' side as Franck Ribery returned to light training on Monday having made good progress in his recovery from a knee injury.