Ramadan Sobhi. Facebook official page Pyramids FC
The South African visitors took the lead in the 56th minute thanks to Ranga Chivaviro's header to stun the home side.
The Egyptian side produced a poor performance during the game and seemed disjointed without their veteran playmaker Abdallah El-Saed, whose African season was ended due to a knee injury two weeks ago.
Marumo Gallants succeeded in capitalising on various errors by Pyramids FC backline and their keeper.
It was a miss-timed jump from Ahmed El-Shennawi, a recurring problem of late for the Egypt international, that allowed striker Ranga Chivaviro to score easily in an empty net.
The visitors had several other clear goalscoring opportunities but lacked the cutting edge to convert.
Pyramids FC will need to avoid a goalless draw in the second leg in South Africa next week to advance to the next round.
(For more sports news and updates, follow Ahram Online Sports on Twitter at @AO_Sports and on Facebook at AhramOnlineSports.)