Fans of Greek Cup finalists Panathinaikos and PAOK threw flares and clashed with police inside the Olympic stadium ahead of the game on Saturday, delaying the kick-off.
More violence during the game then led to the match being suspended.
Violence broke out an hour before the match was due to start as spectators began arriving at the stadium.
Panathinaikos and PAOK fans tried to enter the area of empty seats separating fans and riot police responded with tear gas to break up the crowd.
Greek soccer has been plagued by violence on and off the pitch and authorities have repeatedly promised to clean up the game. Fights between football fans are frequent before or after a game and it is not uncommon for a match to be disrupted by crowd trouble or a pitch invasion, despite the heavy fines.
The government has tightened rules to combat violence at sports events following the killing of a 19-year-old soccer fan this year in what was believed to be an attack by rival supporters.Â
In the match itself Panathinaikos took a 1-0 lead through Aitor Cantalapiedra's 34th-minute penalty. However, the match was then suspended after the scorer appeared to be hit by a missile thrown from the stands after players celebrated near the PAOK fans.
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