The win gave them 39 points after 15 matches, three more than second-placed AEK Athens who were held to a goalless draw by fourth-placed Xanthi.
The only other winners in the top six were third-placed Panathinaikos, who prepared to face Olympiakos in a big derby match next weekend with a 3-0 win over Larissa.
Fifth-paced PAOK play Apollon Kalamaria on Monday while Iraklis in sixth were held to another goalless draw by bottom club Kallithea.
Olympiakos had to work hard for their win and had to do without Rivaldo for much of the game after the Brazilian limped off after just 34 minutes.
The game looked to be heading for a draw until two minutes from time when Ieroklis Stoltidis volleyed home from close range.
Panathinaikos looked refreshed by the winter break and shrugged off all of the speculation surrounding the future of coach Alberto Malesani by seeing off Larissa with some ease.
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Gekas, who has been out of favour in the Panathinaikos frontline recently, added a second in the 77th minute and 20-year-old Alexandros Tziolis finished things off with a superb long-range effort five minutes later.
AEK's run of nine successive wins came to an end when they were frustrated by a Xanthi team that had won just one of their previous six.
AEK goalkeeper Stefano Sorrentino produced two outstanding saves to deny Xanthi including an extraordinary reflex effort to deny a close-range header from Paraskevas Antzas.
In the relegation battle, Kallithea picked up a point but there were defeats for Panionios, Akratitos and OFI Crete.
