Former Greece international defender Triainos Dellas put AEK ahead with a first-half header before a second-half brace from former Portsmouth midfielder Papa Bouba Diop sealed a vital win for Manuel Jimenez's Greek Cup winners.
The match was played behind closed doors as punishment for the ugly pitch invasion which marred the Greek Cup final last month.
Panathinaikos, who ended the regular season in second place, have a tough task if they are to overhaul their rivals in the four-team mini league after the Greens went down to a shock 2-1 defeat at Olympiakos Volos.
Sebastian Leto gave Jesualdo Ferreira's team the lead after 33 minutes but second-half goals from Ilias Solakis and Juan Martin condemned Panathinaikos to their second defeat in three playoff matches, leaving them on four points.
Olympiakos Volos prop up the standings with three points.
The next round of matches are scheduled for Wednesday with Panathinaikos hosting Olympiakos Volos while PAOK welcome AEK.
Olympiakos Piraeus sealed their 38th Greek title in March.
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