Pitso Mosimane immediately drafted in Gaston Sirino, Sibusiso Vilakazi, Hlompho Kekana and Mosa Lebusa after the quartet missed last Sunday's Nedbank Cup win over Vaal University of Technology.
The Cairo giants pinned the South Africans in their own half in the earlier exchanges, however, Vilakazi went up at the other end and forced Mohamed El-Shenawy to save for a corner.
Sundowns were given a big scare in the 16th minute after Amr El Solia's header flashed the left-hand post following an in-swinging free-kick.
Sirino soon lined-up a shot from range at the midway point, but the effort flew wide of El Shenawy's goal, whilst Denis Onyango commanded his area well with well-timed punches.
Masandawana managed to hold their defensive lines amidst pertinent pressure from the Red Devils, who launched countless attacks on the opposing goal.
The pressure though finally took its toll on the South African champions after Ali Maaloul cushioned home Junior Ajayi's cross ten minutes into the second stanza for the game's opening goal.
Ahly took complete ascendancy following the front foot and duly grabbed a second after Maaloul fired home from the penalty spot on 68 minutes after Ali Badji went down in the danger area.
Masandawana turned to the bench at the same with their backs against the wall and introduced Tiyani Mabunda for Sirino.
No comeback let alone away goal arrived for the visitors, as Ahly managed the rest of the game for a first-leg triumph with the return-leg set for Tshwane in a weeks time.
Al Ahly SC: El-Shenawy, Fathy, Ibrahim, Metwaly, Maaloul, Afsha, El Soleya, Dieng, El Shahat, Mohsen, Ajayi.
Sundowns: Onyango, Madisha, Arendse, Nascimento, Lebusa, Maboe, Kekana, Jali, Zwane, Vilakazi, Sirino.