Nuremberg, 15th in the league, were eliminated from the competition by Greuther Fuerth – a high-flying second division team which is also a close neighbour – on Tuesday.
According to police more than a hundred Nuremberg fans invaded the pitch at the final whistle in a bid to reach the opposing team's fans. Security officials were forced to use truncheons and tear gas in a bid to separate them.
It comes less than two months after second division Dresden were banned from the 2012-13 edition of the German Cup after their fans prompted violent incidents during a 2-0 defeat to Borussia Dortmund.
German police, referees and football officials have publicly spoken out in recent months about what they say is the worrying trend of increasing fan violence.
In October referees held public protests to confront what they said were increasingly dangerous working conditions. Berlin's football association paused all games for five minutes on one day that month in order to raise awareness about violence against referees.
And in the spring this year, police said hooliganism by football fans was reaching new highs.
They said they were being forced to develop new strategies to deal with the problem.