The attacking midfielder has not made the match squad for Wednesday's Bundesliga encounter as he is yet to fully recover from an injury that has kept him out since January
The Germany international sustained a hip injury in January and has since been out of action for the league leaders.
Gotze recently resumed squad training and Dortmund were hopeful that the attacking midfielder would be match fit in time for the game against Bayern.
However, BVB have now confirmed on their official website that the 19-year-old has not made the match squad for the game at the Signal Iduna Park as he is not fully match fit.
Dortmund defend a three-point lead in the table over their rivals in Wednesday evening's encounter. The match kicks off at 20.00CET.