The Namibian veteran received two cautions before the end of the first half after losing his head in a personal tussle against Clayton Daniels.
Jabulani Shongwe got the game's decisive goal with a beautiful right-footed finish into the top-right corner in the 41st minute.
Despite their man disadvantage, the Clever Boys continued to create the better chances and were deserved winners on the night.
Discounting Papy Faty's early attempt there was nothing to write home about in the early exchanges, with the most exciting moment of play an off-the-ball scuffle that resulted in Michael Boxall and the Burundi international being cautioned.
While possession was equally shared between the two sides, Wits looked the more dangerous and Daine Klate was unlucky to lose his footing, having found space inside the area following a quick counter in the 19th minute.
SuperSport were finding it hard to find a way past a stubborn Clever Boys defence, with Moeneeb Josephs untested in the opening half-hour.
At the other end Thulani Hlatshwayo forced Ronwen Williams into an easy save in the 37th minute with the defender failing to conjure any power on the ball having found a pocket of space inside the area.
Bidvest Wits, though, would be rewarded soon after with Shongwe opening the scoring on the night with 41 minutes on the clock.
The Bafana Bafana midfielder showed the confidence of a man in form, charging into the area before stepping past Bongani Khumalo and curling the ball into the back of the net.
Having seen his side take the lead, Gavin Hunt would've had his team talk worked out, but the former Matsatsantsa coach had to change his speech heading into the tunnel as Botes was sent off following a second bookable offence.
Desperate times call for desperate measures. Eager not to lose two games in succession against fellow title contenders, Gordon Igesund introduced David Mathebula and Kingston Nkhatha early in the second half as he searched for an equaliser.
Still SuperSport struggled to create chances with Thuso Phala seeing his shot in the 71st minute fly just over before a superb bit of defending by Markus Lecki denied Jeremy Brockie a shot at goal with four minutes of regulation time remaining.
The New Zealand international controlled the ball on his chest inside the area and looked odds-on to score from five yards out, but the young defender was alert to the danger to clear at Brockie's shoelaces.
The win moves Bidvest Wits top of the standings with four wins from five matches.