The right-back was set to remain in Munich instead of making the trip to Dortmund as he had been suffering from stomach problems.
Jerome Boateng was also a doubt but takes a place on the bench, while Niklas Sule lines up in defence alongside Mats Hummels.
Dortmund line up with Nuri Sahin and Mario Gotze in reserve, with Julian Weigl and Gonzalo Castro playing instead.
Omer Toprak keeps his place in the centre of defence in place of the suspended Dan-Axel Zagadou, while Marcel Schmelzer returns after coming off the bench against APOEL Nicosia in Wednesday's Champions League game.
Jupp Heynckes' side are three points ahead of their hosts heading into the game and on a six-game winning streak in all competitions.
Bayern Munich XI: Ulreich, Kimmich, Sule, Hummels, Alaba; Martinez, Thiago, James, Robben, Coman, Lewandowski
Bayern bench: Starke, Rafinha, Boateng, Rudy, Vidal, Tolisso, Wriedt
Borussia Dortmund XI: Burki, Bartra, Sokratis, Toprak, Schmelzer, Weigl, Kagawa, Castro, Yarmolenko, Aubameyang, Pulisic.
Dortmund bench: Weidenfeller, Toljan, Guerreiro, Sahin, Sancho, Gotze, Schurrle.