كتب : Omar AbdelAziz
George Georgiadis gave PAOK the lead in the 18th minute before Dimitrius Papadopoulos equalized for Panathinaikos in the 35th minute from the spot.
Midfielder Sotirios Balafas sealed the precious victory eight minutes after re-start.
Egyptian defender Amir Azmi played for the majority of the game before being replaced eight minutes after the hour mark.
The result put PAOK in fourth place of the league table with 29 points while Panathinaikos lie third on 41 points.
The victory comes one week after Panathinaikos dumped PAOK out of the Greek Cup with a 4-3 aggregate victory on Saturday.