Panathinaikos seal Champions League spot
The France marksman, who scored 20 league goals during the regular season, struck twice in nine minutes during the second half as the Greens moved on to 13 points from six matches.
The game at the Olympic Stadium was played behind closed doors as AEK completed their third and final match without any fans as punishment for the crowd violence which marred the Greek Cup final involving the Yellows and Atromitos last month.
The result means Jesualdo Ferreira's team will now enter the Champions League third qualifying round where they will attempt to win a place in the lucrative group stage.
PAOK Salonika finished second in the four-team mini league with 12 points after a 5-1 home win over Olympiakos Volos.
Greece's representatives in the Europa League will be Cup winners AEK, PAOK and Olympiakos Volos.
Champions Olympiakos, who wrapped up the title in March, automatically qualify for the Champions League group stage.