Stadium announcers in Dortmund and Berlin threatened calling the games off unless the banners were removed, while Bayern Munich's match at Hoffenheim finished in farcical scenes as the players from both sides kicked the ball to each other to wind the final 10 minutes off the clock.
The interruptions are broadly symbolic of a fierce debate in German football between fans of traditional clubs and those of newer teams who have been bankrolled by investors and private owners.
The protests have targeted the German Football Association (DFB) and its decision to hand down a two-year ban to Dortmund fans from travelling to the club's games against Hoffenheim, after the Dortmund fans held up offensive banners.
The move has however only served to call fans into action over what they see as "collective punishment". The fans won support from Cologne captain Jonas Hector after Saturday's victory over Schalke, as he asked why should "20,000 people who have supported us for the entire 90 minutes be punished for the actions of a few?"
Much of the rancour has been directed at Hoffenheim benefactor Dietmar Hopp, who has been widely criticised by fans after circumventing the league's fan-ownership laws in order to invest more than 350 million euros ($387 million) into the village club, bringing it into the first division in the process.
Offensive banners critical of Hopp have found their way into the stands in several fan blocks in recent weeks, including depictions of Hopp's face in crosshairs while also calling him a "son of a bitch".
Bayern Munich chairman Karl-Heinz Rummenigge stood side-by-side with Hopp during Saturday's fixture, shaking his head and pleading with his side's fans to remove the banners.
After the game, Rummenigge said he was "deeply ashamed" of the fans. "I apologised to him (Hopp), but there are no excuses for what the fans did."
Hopp himself said on Sunday that he had "no interest in dealing with people who have insulted me massively for years and want no consensus at all".
While he thanked the players on Saturday for taking a stand, he said similar stances needed to be taken against anyone "sewing the seeds of hate".
"Insults against everyone are to be condemned, no matter where and in what form. All racist and homophobic insults must be punished with all consequences."
There are however some in German football who feel that interrupting and even abandoning matches is not the right cause of action as it will only serve to rile up supporters.
Union Berlin boss Oliver Ruhnert, whose side's home match against Wolfsburg on Sunday was delayed for more than 10 minutes due to banners targeting Hopp, said he wanted to avoid a situation "where I have to interrupt each and every game soon. I see that quite critically."
While saying that banners such as those targeting Hopp were a "no go", he believes the DFB need to act in a less antagonistic fashion and prioritise opening up a dialogue with supporters.
"The fans have a right to objectively criticise. It is always about being in conversation with one another and communicating."
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