Huntelaar, last season's top Bundesliga scorer who also grabbed the winner in their 2-1 Champions League victory at Olympiakos on Tuesday, missed training along with Jones on Thursday.
"It will be tight getting them ready to Saturday," coach Huub Stevens told reporters.
The Dutch coach also said Romanian Ciprian Marica was recovering from a groin injury but would not be fit in time for the game.
Schalke are two points behind Bayern, who lead the standings with a maximum nine points from three games.
- Huub Stevens