Guardiola, who won 14 of 19 possible titles in his four years at Barcelona, also cast doubt on the participation of midfielder Bastian Schweinsteiger, who only recently came back from injury.
"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 told reporters on Friday.
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."