The January 16 match was delayed for 30 minutes after a small section of the Panthessaliko stadium in Volos was damaged by fire as authorities fought running battles with PAOK supporters trying to enter without tickets.
The Greek Super League said the Salonika club would have to play the second leg of their Greek Cup quarter-final against Olympiakos on February 2 in an empty stadium.
Crowd trouble has tarnished Greek football already this season.
Panathinaikos had to play two games behind closed doors in December after fans chased the players off the pitch and pelted them with missiles following a surprise home defeat.
Larissa players and staff were stranded inside their team coach for four hours on January 5 when fans set up a blockade of bonfires following a heavy loss.
