Two players from Portuguesa were sent off amid the confusion which started when Gremio were awarded a decisive penalty 10 minutes from the end of Saturday night's game.
Portuguesa, who had fought back from 2-0 behind to draw 2-2, were angry about the decision but their protests quickly died down.
However, just as Gremio forward Kleber was about to take the kick, Portuguesa's Bruninho walked into the area to point out that the ball was not properly on the spot.
He was shown his second yellow card of the game and sent off, infuriating Portuguesa who surrounded the referee and gesticulated angrily.
The referee signalled for police to come on to the field and six officials with riot shields and truncheons formed a cordon around him as the protests continued. Portuguesa's Valdomiro was also sent off and Kleber finally took the kick after a five-minute delay, converting it to give Gremio a 3-2 win.
Gremio's victory took them up to second in the table with 34 points, three behind leaders Cruzeiro. Portuguesa were left in 17th place, in the relegation zone.