After a pedestrian start in Orkney, Stars grabbed the lead at their first attempt when Makhehlene Makhaula got the better of Moeneeb Josephs with a strike from range in the 24th minute.
It was a stop-start affair for the remainder of the first half as the two sides engaged in a physical bout, with referee Victor Gomes flashing his yellow cards.
The hosts got the second half off in similar fashion to their first half exploits as Thokozani Sekotlong narrowly missed the target from a set-piece in the 49th minute.
Wits came closest just before the hour-mark as Vincent Pule's cross headed for goal but was denied by the crossbar, with Thela Ngobeni left to watch on before Stars' defence cleared their lines.
Stars doubled their lead in the 65th minute as Phumlani Ntshangase was dispossessed in a dangerous area by Sifiso Mbhele, who proceeded towards goal and hit the upright, but Mohammed Anas was on hand to tap home the rebound.
The visitors pulled one back with under 15 minutes to go as Cuthbert Malajila tapped home from close range.
Three minutes later, Gomes flashed his red card after adjudging Sifiso Myeni to have been the last man in defence when impeding Anas. However, TV replays showed Thulani Hlatshwayo to be in line with the play.
Ea Lla Koto restored their two-goal cushion in the final minute of regulation time, as Anas broke away on the counter and picked out Sinethemba Jantjie, whose strike beat Josephs at the near-post.
The result sees the Free State-based side maintain their unbeaten run at home to Wits, stretching it to six games in all competitions dating back to October 2013, while also moving two places up into 13th place.
Wits remain at the summit, two points ahead of champions Mamelodi Sundowns with two games remaining.