Wits pulled out the big guns for their crunch first-leg clash, with Moeneeb Josephs and Thulani Hlatshwayo handed starting berths.
Striker Lehlohonolo Majoro, who missed numerous chances in the previous clash against Primero de Agosto in the CAF Champions League, started from the bench.
Wits took an early lead after a defensive error brought in Daine Klate, who obliged with an easy tap-in at the back post.
The former Bafana Bafana international then looked to turn provider after picking out Thobani Mncwango at the far post, but the latter failed to get his header on target minutes later.
The response from the Nigerians was instant, with Ibrahim Mustapha slotting coolly past a hapless Josephs from an in-swinging delivery.
Wits looked to regain the lead immediately, with Sifiso Hlanti sent clear to play in Sifiso Myeni, who produced a volley inside the box with the follow-up attempt from Eleazar Rodgers going wide.
Mustapha had a decent chance after getting on the end of a counter-attack to only head wide after 21 minutes.
Klate delivered another inch-perfect cross from the left, which fell to Mncwango once more but as with his earlier attempt, was unable to find the target.
The Students nearly regained their lead after Reeve Frosler’s shot was scrambled off the goal-line at the start of the second half.
Afelokhai came up with another outrageous save following Rodgers' attempt on 55 minutes, with the game swinging from one end to the other.
In the closing stages, Majoro replaced Klate as the hosts searched for the elusive winner for a reasonable return-leg.
It was forthcoming, and as a result they have to take a rather slender result to Aba with the Elephants granted the advantage in the overall sequence.
Wits: Josephs, Gyimah, Hlatshwayo, Khumalo, Klate, Rodgers, Hlanti, Claasen, Mncwango, Frosler, Myeni
Subs: Peters, Ntshangase, Monare, Ritchie Pelembe, Majoro, Pule.
Subs: Governor, Omofoman, Chukwude, Ibenegbu, Farouk, Ezenwa, Uche.