Only four minutes of the preliminary round second leg remained and a penalty shootout was looming when Zimbabwean Cuthbert Malajila scored the tie-clinching third goal after a goalmouth scramble.
Constantly criticised during short-lived campaigns in the secondary CAF Confederation Cup for selecting weakened teams, Wits coach Gavin Hunt once again fielded a virtual 'B' team for an African game.
He made seven changes to the side that started a domestic league victory over Orlando Pirates three days ago and some of the defensive replacements lacked pace.
It was the attacking strength of the South Africans that squeezed them through with Daine Klate and Sifiso Myeni scoring either side of half-time.
Sylvain Phileas reduced the deficit on the night to one goal and levelled the tie on aggregate when he scored 11 minutes from time.
Malajila then rescued the Johannesburg outfit from potential embarrassment and secured a mid-March showdown with Ahly over two legs.
ZANACO of Zambia did well to defeat APR of Rwanda 1-0 in Kigali after being held to a goalless first-leg draw at home.
Taonga Bwembya scored the crucial goal during the first half to clinch a last-32 clash with Young Africans of Tanzania.
The Dar es Salaam club were surprisingly held 1-1 at home by Ngaya Mde of the Comoros having won the first leg 5-1 in the Indian Ocean island state.
Other clubs to qualify for the round of 32 included Coton Sport of Cameroon, CNaPS Sport of Madagascar, AS Tanda of the Ivory Coast and Al Merrikh of Sudan.