They remain at the top of the table with 47 points, four points ahead of Ahly, who could narrow the gap if they manage to beat Harras El-Hodoud later in the day.
After a dull first half, Pharco FC striker Ahmed Sherif opened the scoring in the 55th minute, while Mahmoud Emad doubled the lead 11 minutes later. Substitute winger Ibrahim Adel narrowed the gap in the 75th minute, but Amr Nasser restored Pharco FC's two-goal advantage by converting a penalty with six minutes remaining.
Striker Marwan Hamdi added a second for Pyramids FC in injury time, but it was insufficient for the table leaders, who suffered their first defeat in the playoffs.
Pyramids FC will face a tough clash against NBE Club on Friday.
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