An abusive banner targeting Hoffenheim’s billionaire owner Dietmar Hopp saw the referee stop the match as Bayern’s players, flanked by manager Hansi Flick, ran over to remonstrate with the supporters.
However, the unrest did not dissipate and both teams were ordered down the tunnel.
The game eventually resumed after a 20-minute stoppage, with extraordinary scenes unfolding as the players ran down the clock without any hint of playing properly.
Both goalkeepers stood near the centre circle as the players passed and chatted their way towards the full-time whistle.
After the match, the teams and staff gathered on the pitch to salute Hopp, who received a rapturous ovation from the home fans.
Hopp has been a lightning rod for some German fans, who oppose the way he used his wealth to help Hoffenheim climb through the lower leagues to the Bundesliga with consecutive promotions more than a decade ago.
A similar insulting banner led to a Borussia Dortmund fans' ban in Hoffenheim for two seasons and 50,000 euro fine earlier this month.
"I am deeply ashamed for the behaviour of these people. That is inexcusable. It is the ugly face of football," Bayern CEO Karl-Heinz Rummenigge, who was alongside Hopp after the match, told reporters.
"I have apologised to Dietmar Hopp. We have filmed everything and these people will be held accountable."
Goals from Serge Gnabry, Joshua Kimmich, Joshua Zirkzee, Philippe Coutinho (two) and Leon Goretzka had early wrapped up a commanding win for the Bundesliga leaders.
With additional reporting from Reuters