The kick-off was delayed for 30 minutes after a small section of the Panthessaliko stadium in the Thessaly city of Volos was damaged by fire as authorities tried to remove PAOK supporters who attempted to enter without tickets.
PAOK fans hurled missiles and flares at the police who eventually managed to get the situation under control and disperse the crowds using tear gas.
"These images are not football, the police were right to act as they did," Olympiakos Volos president Achilleas Beos told reporters.
"Everyone has a responsibility to fight this problem but at some point those who should must find a solution to this unhealthy situation."
Crowd trouble has again tarnished Greek football 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 as fans set up a blockade by lighting bonfires around the bus following a heavy loss.
PAOK won 3-0 on Saturday with goals by Alves Lino, Vierinha and Dimitris Salpigidis, lifting the Thessaloniki club to third in the table with 30 points from 18 matches.
Olympiakos Pireaus extended their lead to eight points after coming from behind to earn a 4-2 home win over Panserraikos.
Former Liverpool winger Albert Riera was on target twice, scoring with a penalty and a brilliant free-kick, as the Spaniard continues to resurrect his career. Serbian striker Marco Pantelic also got a brace for Ernesto Valverde's side.
The win moved the Reds on to 45 points after 18 matches.
