The two sides played out time in bizarre scenes after the match was twice interrupted and the players were taken off the field.
Insulting chants and banners were directed at Hopp, an unpopular figure due to his financing of the home club, from spectators in the away end on Saturday.
The game was paused as a banner was unveiled in the final 20 minutes, with Bayern players and officials pleading with supporters to stop so the game could continue.
Play resumed for a brief period, before referee Christian Dingert directed the teams towards the dressing rooms due to the continued protests, prompting Oliver Khan and Hasan Salihamidzic to head onto the pitch and also implore with followers of the Bavarian giants.
The sides eventually returned to the field, and all 22 players convened in the center of the pitch to see out time with a round of applause while passing and juggling the ball between themselves and clapping along with fans.
Hopp also headed onto the pitch and shook hands with Bayern officials and the referee, who finally blew up in a strange conclusion to a one-sided match.
Leaders Bayern put Hoffenheim to the sword, adapting seamlessly to life without the injured Robert Lewandowski as 18-year-old Joshua Zirkzee scored on his first Bundesliga start.