The visitors were unhappy with the refereeing in the game where they trailed Panathinaikos by 15 points at half-time.
"We have seen it many times. We are disgusted and enough is enough," Olympiakos general director Christos Stavropoulos told reporters before the team boarded a bus and left the Olympic indoor arena.
"We should have left earlier. The Greek state needs to take measures to clean this filth."
His team are leading in the Greek league, a point ahead of Panathinaikos, who have a game in hand.
The referee noted in his match report the team's refusal to play on after the break and awarded the game to the hosts. Under Greek basketball rules a team walking out of a match can be deducted up to six points.
The bitter rivalry between the clubs was fanned further when controversial Panathinaikos president Dimitris Giannakopoulos, who in the past has verbally assaulted Olympiakos players, dropped a red women's underwear on the empty visitors' bench when the game was awarded to his team.
(Reporting by Karolos Grohmann; editing by Sudipto Ganguly)
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