Coloured flames and smoke lit up the section of Ostseestadion housing the visiting Hertha supporters as several flares and fireworks were let off in the second half.
Referee Robert Hartmann had earlier briefly halted the match due to missiles being thrown onto the pitch, before the problems escalated.
Fireworks were aimed from the Hertha section towards Hansa fans, while seats were said to have been set on fire and flags burned among both sets of supporters.
The players and officials headed for the tunnel for a period of 15 minutes in the second half, with the scores at 0-0, before the game resumed after police stepped in to further segregate the supporters.
Hertha went on to win 2-0 thanks to goals from Mitchell Weiser and Vedad Ibisevic in the closing minutes.
Earlier, Schalke progressed from its clash with BFC Dynamo, Yevhen Konoplyanka's double securing a 2-0 win.
Nurnberg ran out a 2-1 winner Duisburg and Paderborn saw off St Pauli by the same scoreline.