Wits, with 51 points from 25 matches, moved a point ahead of Sundowns at the summit courtesy of Ben Motshwari's 42nd minute headed goal off a cross from Sifiso Myeni at Bidvest Stadium.
The second period failed to produce goals but delivered late dismissals for both sides, as substitutes Fares Hachi and Daine Klate earned second cautions in the final 10 minutes.
In a tense affair, Wits threatened midway through the opening half, but returning midfielder Thabang Monare's effort from distance was nicely dealt with by Ugandan goalkeeper Denis Onyango.
Soon after Mogakolodi Ngele dragged a shot wide for the Students, while at the other end Bafana Bafana newcomer Percy Tau narrowly failed to get on the end of Khama Billiat's ball across the face of goal.
Motshwari then gave the Clever Boys the lead with a commanding header shortly before the break.
Themba Zwane nearly equalised on the stroke of half-time but his close-range strike was foiled by the upright, and that was the closest it came for the Brazilians to find a way back.
Regarding the other teams still in the hunt for championship honours, Cape Town City slipped to third spot with 49 points from 26 games following an earlier 1-0 defeat at top-eight hopefuls Maritzburg United.
Fellow contenders Kaizer Chiefs trail the Students by five points after conceding a last-gasp equaliser in a 2-2 draw with SuperSport United on the weekend.