Olympiakos' American centre Kyle Hines was struck on the back with a flare in the warm-up at the neutral Elliniko Indoor Court venue with a restricted crowd of just 1,800 supporters.
Hines was not seriously injured, however, and was able to start the match.
But with Panathinaikos 26-17 ahead 13 minutes into the Athens derby encounter, the match referee ordered the players off the court after fans proceeded to fire flares at each other and rip up seats before spilling on to the court to fight running battles with each other and police.
After a 30-minute delay while authorities got the situation under control, organizers announced that the stadium would be completely cleared out and that the match would continue in front of Hellenic Basketball Federation officials, club officials, journalists and security staff.
Both teams eventually reappeared to begin their warm-up for the game to restart, 55 minutes after they were ordered into the dressing rooms.