Bayern came into the match in third spot and with three changes in Jerome Boateng, Thiago Alcantara and Leon Goretzka after the victory over Vfl Wolfsburg.
The Bavarians made a quiet start, but Ivan Perisic particularly and Robert Lewandowski put the home side in a spot of bother with a couple of dangerously looking attempts.
Hertha then applied a period of sustained pressure on 27 minutes but Davie Selke failed to execute sufficient power on Lukas Klunter's floating delivery into the danger area.
Phillipe Coutinho made a late run in the area to meet Thomas Muller's cross ten minutes before halftime, but the Brazilian failed to put his side ahead with a tame side-foot delivery.
A close call seven minutes from halftime saw Jordan Torunarigha scrambling across the goal-line to clear Perisic's nod-back to safety after a floating cross into the area from Muller.
Regardless, Bayern went ahead following the 60th minute when an unmarked Muller thumped home a half-volley after being setup by Perisic.
The champions went further ahead after a foul in the area from Klunter on Goretzka led to a spot kick, which Lewandowski tucked home with pure composure on 73 minutes.
Alcantara handed Bayern a third three minutes later when Goretzka threaded a through pass through to the area for the former Barcelona man who slammed into the top left corner.
Bayern made their final eight minutes from time, as Coutinho's day ended with Mickael Cuisance his replacement.
There was time for more as Perisic capped a fine afternoon when he connected with Muller's delivery for a towering header in the final minute, thus taking Bayern to second spot.