Bayern confirmed its captain sat out Thursday's session at Sabener Strasse because of a gastro-intestinal infection.
Neuer, 33, has been an ever-present for Bayern in the Bundesliga and UEFA Champions League this season.
There was better news for head coach Hansi Flick as Joshua Kimmich and Alphonso Davies were back among the first-team group having been laid low by a cold and an ankle knock respectively.
Following last weekend's 0-0 draw against second-place RB Leipzig, Bayern retain a slender one-point advantage as they pursue an eighth consecutive Bundesliga crown.
Flick's side resumes its UEFA Champions League campaign with a last-16 trip to Chelsea on February 25.