Thembinkosi Fanteni had given the visitors an early lead, but Ugandan international defender Timothy Batabaire's second half strike earned the Clever Boys a point.
The visitors opened the scoring 10 minutes in, when Fanteni's right-footed shot went in, bottom left.
Fanteni almost made it two with a header from Lebogang Manyama's free-kick, but hit wide.
Two minutes later Wits were looking to get into the game and had a chance when midfielder Sibusiso Vilakazi's left-footed shot from 25 yards out on the wing went over the bar.
When the second half commenced Wits substitute Miguel Timms had a right-footed shot from 30 yards that went over the bar. But Roger de Sa's young side would finally equalise in the 59th minute.
Asive Lange's inswinging corner from right byline found Batabaire, who drilled a right-footed shot into the bottom corner from 12-yards out to make it 1-1.