A host of alterations from the Bavarians after their DFL-Supercup success saw a debut for fullback Chris Richards as Alphonso Davies got a rare start while Serge Gnabry returned.
Bayern dominated the earlier exchanges, with Robert Lewandowski, Thomas Muller and Leon Goretzka having the visitors on the back-foot from their intelligent off-the-ball running.
The Bavarians didn't wait long to go ahead though when Lewandowski slammed home a cutback in the area five minutes to halftime after Alexander Schwolow parried the Pole's initial effort.
Bayern tried to find something from range on the stroke of halftime, but Schwolow rose to the fore to parry Gnabry's thumping strike.
The visitors fell further down six minutes from the break after Lewandowski beat one challenge in the area to slam Richards' cross into the bottom-left corner.
Hertha opened up a little later through the interventions of Matheus Cunha, but he had Bayern goalkeeper Manuel Neuer up to the task whilst the rebound narrowly escaped Jhon Cordoba.
The away side were back in the match 59 minutes in after Cordoba delivered a powering header beyond Neuer after landing onto Cunha's supply.
Bayern targeted a conservative conclusion and such introduced Benjamin Pavard, Jamal Musiala, Corentin Tolisso following the latter stages.
Cunha however brought his side level inside 71 minutes when he charged in from the left before beating Neuer with cool composure after exchanging passes with Krzysztof Piatek.
Prior to consecutive misses, the hosts regained the lead five minutes from time as Lewandowski completed his hat-trick when he reacted to Muller's knock down off a free-kick to roll into the net.
Hertha remarkably levelled in the last two minutes as Jessic Ngankam took Maximilian Mittelstadt's into his stride to head past Neuer.
The treble champions would have the last laugh though when Lewandowski netted from the penalty spot after he went down in the area, leaving the visitors heartbroken.