After Hamburg-based St Pauli, who are third in Germany's second division, came away with a win from Rostock, who are third from bottom, angry home fans clashed with police leading to 33 people being charged on Saturday night.
Around 2,000 officers were used to police the game as Hansa fans vented their frustrations as a police patrol car and three buses used to transfer St Pauli fans were pelted with stones.
The match had been halted for 10 minutes in the first half by the referee after Rostock fans set off smoke bombs and firecrackers after their team fell behind.
The game had already been briefly interrupted earlier when around 100 St Pauli fans stormed an entry gate to enter the part of the stadium for away fans.
After Dresden fans rioted recently at a televised cup match in Dortmund, the German Football Federation (DFB) are sure to announce tough sanctions against Rostock, but the north German club begged for help in a press release.
"We ask the federation, the politicians and the judiciary service not to leave us clubs alone with society's problems," read the statement after more than 5,000 euros worth of damage was done to property.