Ahmed Hegazy grabbed the only goal of the game in the second half as the Clever Boys defence were kept busy for the entire match, with Al Ahly goalkeeper Sherif Ekram seeing out the 90 minutes untested.
A tighty contested first-half ended goalless as the Wits defence held firm to keep the home side at bay.
However, Al Ahly did have the ball in the back of the net in the 20th minute, when Moamen slotted home from close range, but the linesman had flagged for offside before the cross was delivered.
Wits had a chance to open the scoring in the 37th minute, but Phakamani Mahlambi opted to shoot when a pass to Gabadinho Mhango in space would have been a better option, as the teenager's effort missed the target.
The hosts got off to a good start in the second stanza as Amr Gamal struck the woodwork just two minutes after the restart.
Al Ahly's relentless poressure finally paid off as Ahmed Hegazy headed home the opener from a conrer in the 57th minute.
Moeneeb Josephs pulled off a stunning double save to keep the score unchanged in the 67th minute, after a good counter-attack from the hosts.
A minute later Thabang Monare then took the reponsibility upon himself to have a go from distance, but his curling effort was swallowed up by Sherif Ekramy.
The Red Devils continued to push Wits back into their own third as they looked to stretch their aggregate lead, but Hunt will be proud of his defence who held firm.
The second leg will be played at the Bidvest Stadium next week Sunday.
Al Ahly XI: Ekramy, Maloul, Saad, Hegazy, Hany, Fathy, Ghaly, Moamen, Abdallah, Ajai, Amr.
Al Ahly subs: Elshannawy, Naguib, Ashour, Soliman, Moteab, Hamoudi, Coulibaly.
Bidvest Wits XI: Josephs, Allie, Hlatshwayo, Mkhwanazi, Hlanti, Mlambo, Monare, Scott, Klate (Malajila 68'), Mhango, Mahlambi.
Wits subs: Keet, Myeni, Frosler, Malajila, Rogers, Ngele, Pelembe