Both players were forced off through injury during Tuesday's friendly against Liverpool and the club confirmed on Wednesday that they would not be available for the German champions' trip to DFB Cup winners Dortmund.
Thiago suffered an abdominal injury and was replaced by Renato Sanches after only 21 minutes but there may be more concern over new signing James.
The Colombian international's competitive debut for Bayern is set to be delayed as the club said they will have to do without him "in the coming weeks" after a medical examination revealed that he had damaged his right thigh muscle.
It is now unclear if he will be fit to play in Bayern's league opener against Bayer Leverkusen on August 18th.
David Alaba, who was also substituted on Tuesday, will train individually on Thursday before it is decided if he too will miss Saturday's Supercup game.
After Tuesday's game Bayern boss Carlo Ancelotti suggested that centre back Jerome Boateng and winger Arjen Robben could still return from injury to play some part in this weekend's curtain raiser for the new German season.
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