Haris Mavrias scored after 10 minutes and Greece striker Nikos Karelis struck in the 28th to seal a comfortable home win in front of a sold-out Apostolos Nikolaidis Stadium crowd.
The result moved Panathinaikos on to 14 points and means they are now mathematically assured of a place in the third qualifying round of European football's elite club competition.
The Greens have been on top form during the end of season, four-team mini-league playoffs after finishing the regular season as runners-up behind Olympiakos Piraeus, who qualified for the Champions League group stage with their 42nd title win.
The Panathinaikos fans have also been boosted by local media reports that Ghana midfielder Michael Essien is due in Athens this week with the view to joining the club.
The 32-year-old former Chelsea and Real Madrid midfielder is out of contract following an 18-month spell at AC Milan.
Asteras Tripolis are in second place in the playoffs table with six points after winning 1-0 against bottom side Atromitos, who have two points, on Sunday. PAOK are third with four points.
There is still plenty to play for with the team that finishes second going into the Europa League group stage, while the sides coming third and fourth enter that competition in the third and second qualifying rounds respectively.
(Editing by Ken Ferris)
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