The Germany international has not travelled with his Bayern team-mates ahead of the meeting at Westfalenstadion because of an upset stomach.
Kimmich is yet to miss a Bundesliga fixture for the Bavarian club, scoring once and registering three assists in his 10 league outings, but is likely to be replaced by Rahinha for the upcoming game.
Jerome Boateng may also be unavailable to Jupp Heynckes, though the 29-year-old has made the trip and will be assessed in a series of tests before kick off.
Bayern will also be without Manuel Neuer, Thomas Muller, Juan Bernat and Franck Ribery, though Dortmund have a string of injury issues themselves.
Erik Durm, Marco Rues, Sebastien Rode and Lukas Piszczek are all sidelined through injury, while Dan-Axel Zagadou will miss the game through suspension.