Aue won 2-0 at home on Friday in Germany's second tier Bundesliga against ambitious RB Leipzig, who are sponsored by Austrian energy drink company Red Bull.
But home fans marred the victory by displaying several derogatory banners aimed at Mateschitz and his club.
Seventh-placed RB Leipzig is hoping for promotion to Germany's top tier this year, but is unpopular with German football fans due to the millions of euros invested by the drinks company.
"Out of Austria, only the best for Germany," read the text on one banner, under a drawing of Mateschitz dressed in a Nazi uniform, referring to Austria-born Nazi dictator Adolf Hitler.
Another read: "An Austrian calls and you follow blind, every child knows how that ended. You would have made good Nazis," aimed at the RB Leipzig club.
Aue are likely to be fined by the German Football Association (DFB), who are expected to investigate the matter.
"It's a mess, we strongly distance ourselves from the banners," Aue's president Helge Leonhardt said. "Three points won, but in the end a lot of prestige and recognition lost!"
The club put out an official statement distancing themselves from the banners. "We condemn these banners in the strongest possible terms," read the statement.
"We want nothing to do with people who bring these banners and signs, with such despicable content, into our stadium.
"A minority of fans ensured that there was a nasty taste left after a successful evening for Erzgebirge Aue.
"We want to apologise to RB Leipzig for this."