Belgian striker Kevin Mirallas, the Super League's top scorer, was the match-winner with his 19th goal of the season, sidefooting a measured finish into the bottom corner after being released through the middle by Jean Makoun.
With second-placed Panathinaikos also winning 1-0 at home to Aris Salonika the result preserved Olympiakos' four-point lead.
However, the gap is in effect 10 points after Panathinaikos were docked three points and Olympiakos were awarded a 3-0 win over the Greens as punishment for the abandoned Athens derby between the clubs a fortnight ago due to crowd violence.
Panathinaikos have appealed the decision made by the Super League's disciplinary committee and their case is set to be heard next Wednesday by the Hellenic Football Federation, although it is unlikely that the sanctions will be reversed.
The Super League does not plan to verify the league table until after the outcome of the appeal is known, but that did not stop Olympiakos' players doing a celebratory jig in the centre of the Panaitolikos pitch after the final whistle.
"At such moments the atmosphere is always happy, this was a difficult season and one of the toughest title races I've been involved in," Olympiakos captain Vassilis Torosidis told reporters.
"We lost our way a bit in January which is normal - no team in the world can always be at their best. Unfortunately, we picked ourselves up and kept going and for me the depth of our squad was the decisive factor for us this season."
Panathinaikos played in an empty Olympic Stadium - the first of four matches they must play behind closed doors - as punishment for the trouble in their clash with Olympiakos.
The Greens were also fined 252,500 euros and will be docked two points in next season's league campaign.
Hungary striker Gergely Rudolf scored the only goal of the game to clinch victory for Jesualdo Ferreira's Panathinaikos team, who must now focus on the end-of-season playoffs to battle for a place in the Champions League qualifiers.
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