The Bavarians made just two changes in Bouna Sarr and Leon Goretzka, while Mats Hummels, Marco Reus and Jadon Sancho got a recall from the Black and Yellow.
Following a bright start, Lucas Hernandez's pin-point cross picked out Robert Lewandowski who slipped in Serge Gnabry to fire into the side-netting after taking possession in his stride.
Dortmund were behind midway in the first half when Lewandowski got into the centre of the area to tap home a low cross, but the Video Assistant Referee (VAR) disallowed the strike for offside.
Bayern were forced to a change ten minutes before halftime when Joshua Kimmich limped off following a coming-together and were replaced by Corentin Tolisso.
The Black and Yellow took the lead a minute to the break after Reus directed Raphael Guerreiro's pull back into the top corner.
Bayern restored parity in added time as David Alaba sent a well-worked free-kick from the edge of the area beyond the reach of Dortmund goalkeeper Roman Burki.
The Bavarians took control two minutes after the break when Lewandowski charged the near post to head into the far corner after meeting a cross from Hernandez.
Dortmund were under heavy pressure and should've been trailing by three goals with a low strike from Kingsley Coman minutes later hitting the frame of the post.
Bayern put the clash beyond doubt when Leroy Sane drifted inside from the right ten minutes from time to find the bottom-corner.
A nervy final minutes was on the cards when Erling Halaand beat the offside trap to latch onto a long pass to round Manuel Neuer for a simple finish.
Lewandowski looked to have given Bayern a fourth goal in additional time with a first-time lob in the area, but the Polish striker was flagged for offside as the Bavarians bagged victory regardless.