Robben's status was thrown into doubt for the visit to the Bundesliga leaders when, according to head coach Niko Kovac, he had problems during Thursday’s training session.
Kovac downplayed the issue, telling reporters on Friday “everything is fine” though Robben would test his knee out in training to see whether he could play.
Despite his manager’s hopes, Bayern have announced Robben has not been passed fit to travel, meaning he will sit out the season’s first Klassiker.
The 34-year-old has scored three goals in eight Bundesliga games this season, while adding an assist in three Champions League matches.
He will join Thiago Alcantara, Kingsley Coman and Corentin Tolisso on Bayern's injury list.
Bayern, currently level with Borussia Monchengladbach on 20 points in second, will be looking to close the four-point gap to Dortmund at the top of the table when the two meet at Signal Iduna Park.
The reigning champions had struggled in late September and early October, suffering through a four game winless streak.
However, Kovac’s men have rebounded as the heat turned up on their manager.
Since the most recent international break, Bayern are undefeated, taking 16 points from a possible 18 across all competitions.