Bayern gave Hertha no chance, with Arjen Robben scoring on his league comeback from injury last season after goals from Franck Ribery and Thiago Alcantara.
The two teams were the only ones with a perfect record but Bayern ran roughshod over Hertha from the start.
"This was our best game of the season so far," Bayern coach Carlo Ancelotti told reporters. "I am very satisfied.
"We had key players back in the team with Robben and (Jerome) Boateng. They did not have any problems."
The hosts could have scored twice in the opening three minutes with both Robert Lewandowski and Thomas Mueller missing their point-blank chances.
Ribery, eager to secure a contract extension, did it much better when he weaved into the box, spectacularly shaking off two markers and firing in for the lead after 16 minutes with his second goal of the season.
The Bavarians, with Boateng making his first start since his Euro 2016 semi-final injury in July, had more than 70 percent possession during the one-sided first half.
They took some of the pace out of their game after the break and Hertha carved out a decent chance on the break with Valentin Stocker but Manuel Neuer was on hand to save.
Thiago then settled any nerves, snatching the ball from Hertha's Allan and firing in a low shot for a two-goal lead before substitute Robben curled in a trademark left-footed shot to crown his comeback.
Bayern are on 12 points with Cologne, in second place on 10 after beating Schalke 04 3-1. Schalke are in 17th place after their fourth loss in four Bundesliga matches, with coach Markus Weinzierl under mounting pressure.
Borussia Dortmund are third on nine after Tuesday's 5-1 demolition of VfL Wolfsburg.
Werder Bremen, who sacked coach Viktor Skripnik on Sunday after three straight losses, conceded two stoppage time goals to lose 2-1 against Mainz 05 on interim coach Alexander Nouri's debut on the bench and remain in last place.
Bayer Leverkusen missed yet another penalty, settling for a goalless draw against Augsburg to drop to 12th place on four points.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
