Pharco FC took an early lead in the third minute when defender Abdallah Bakry was found unmarked at the far post from a free kick.
Ahmed Modi secured the victory from the penalty spot in the 86th minute after Pharco striker Ahmed Sherif was brought down in the area.
The hosts had several chances to extend their lead, including a goal that was denied for offside after VAR check, but Zamalek's keeper Mohamed Awaad produced several outstanding saves in an attempt to keep his team in the game.
On the other side Zamalek failed to capitalise on their chances as skipper Youssef ‘Obama’ Ibrahim and youngster Youssef Osama lacked sharpness in front of goal.
Zamalek are scheduled to face Ghazl El-Mahalla, meanwhile Pharco will face Talae El-Gaish.
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