Substitute Anthony Laffor decided the tie in the 75th minute at Lucas Moripe Stadium following a goalless stalemate in the first leg.
The lanky Liberian finished a fine attacking movement which involved touches from Percy Tau, Khama Billiat, Tiyani Mabunda and Sibusiso Vilakazi.
Sundowns will battle Wits for honours at Mbombela Stadium in Nelspruit on October 1. The Clever Boys defeated Cape Town City 3-0 on aggregate in the previous round.
The Brazilians will also look to book their place in the CAF Champions League final on Saturday when they host Zesco United in Atteridgeville. Pitso Mosimane's side lost the first duel 2-1 in Ndola, Zambia last weekend.