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."
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.
