Coach Pep Guardiola, who took over after Jupp Heynckes's record-breaking season with the Bavarians, said the two players were nursing minor injuries from their friendly 2-0 win over Barcelona this week and would not be fit for the first chance of a trophy this season.
"Bastian will travel with us but we do not know yet if he can play. He has only a few training sessions under his belt," the Spaniard said.
Mario Goetze, Bayern's big transfer from Dortmund, will also miss the game as he is still recovering from the muscle injury that kept him out of the Champions League final in May.
The two teams have slugged it out in the Bundesliga in the past three seasons with Dortmund winning the 2011 and 2012 editions and Bayern returning to the top last season, when they also added the Champions League trophy and the German Cup.
Bayern beat Dortmund 2-1 thanks to a last-gasp Arjen Robben goal in the Champions League final in London and also eliminated their rivals in the German Cup quarter-finals.
"You have no excuse if you are Bayern coach," Guardiola said. "A final is a final and you have no second chances on Saturday.
"It is never easy against Dortmund, they play a good game, with a lot of possession. We want to see at what level we are at and plan both for the game and beyond."
For Dortmund coach Juergen Klopp, the early encounter with Bayern has little to do with revenge for the bitter Champions League defeat.
It is more a chance for Dortmund to kick off the season with a bang in front of a home crowd and lift the trophy after two failed attempts in the past two seasons.
"We do not entertain any thoughts of revenge," Klopp said. "We played a great game in Wembley stadium which we could not decide in our favour but from which we learned a lot.
"There is no doubt we will do everything to win this game. It is after all our third straight final but we failed to lift it the past twice," said Klopp.