Youssef Obama opened the scoring in first-half stoppage time (45+2), before Odeh Fakhouri added a second goal early in the second half to seal the points at the 30 June Stadium.
The result keeps Pyramids top of the table with a perfect record of six points from two matches. Mokwena’s side have scored five goals and conceded none so far this season, following their opening 3-0 away win over Ghazl El Mahalla.
The South African coach continues his strong start in charge of the Cairo club as they push for a title challenge in the new campaign.