The win means that the Reds are now tied in first place with Fenerbahce Ulker after both teams scored three wins and one defeat in four games in Group H.
The two leaders meet in Turkey next week.
The lead in Thursday's game see-sawed between the two teams but Olympiakos showed coolness under pressure to tip the balance in their favour in the final minutes.
Vassilis Spanoulis scored 18 points and Rasho Nesterovic chipped in with a very valuable 16 points.
"We didn't start well, they were better with the rebounds but then we balanced that," said Reds coach Dusan Ivkovic.
"We had a bad second quarter but later we had the concentration that we needed to win the match, finally we deserved the win. We lost the first game of the Top 16 but now we have improved and we are in a good moment."
