The result left Sundowns on top of Group B with 11 points after five matches - five points ahead of the Clever Boys.
Wits had a great chance to open the scoring midway through the first stanza, but Mthokozisi Msomi failed to beat Thela Ngobeni from the penalty spot.
The Brazilians, who fielded the likes of Uzoenyi Ejike and Anthony Laffor, then took the lead just before the interval, as Ngubane curled home a stunning effort from 25 yards out.
The Students threatened to pull one back soon after the break, but Toriq Losper's strike was foiled by a fine save from Ngobeni, while at the other end Boalefa Pule denied Thamsanqa Masiya from close range.
Wits, however, equalised in the 65th minute, as Monamodi pounced with a first-time finish into the bottom corner of the net for a share of the spoils.