There was no place in the side for Sunday's match-winner Eva Nga who was once again named on the bench while Thulani Hlatshwayo missed out through suspension.
It was an evenly contested affair in the early stages, as both sides struggled to carve out clear cut chances in the opening 15 minutes.
Ricardo Goss was called into action just before the 20-minute mark, producing a vital interception with Leopards top scorer Mwape Musonda lurking in the six-yard box.
Hunt was forced into a first-half change as Lisakhanya Mlonyeni's first-ever league start ended after 33 minutes due to injury. He was replaced by Keenan Phillips.
While the first half ended goalless, Leopards managed to break the deadlock 10 minutes into the second half thanks to Musonda's finish.
Gavin Hunt responded with a double change as Eva Nga and Mathebula replaced Cole Alexander and Haashim Domingo for the final 25 minutes.
Even with the late introductions from the Clever Boys, Leopards were able to see out the rest of the half and claim a vital win.
Leopards: K. Ndlovu; Mudau, Masia, Gyimah, Zulu; Matlaba, Abubakar, Mokoena, Makgetlwa, Hlongwane; Musonda.
Subs: Jonas, Ndawonde, Ndou, Mashoene, Ng'ambi, Dax, Thutlwa, Khutlang, T. Ndlovu.
Wits: Goss; Macheke, Mlonyeni, Gordinho, Ritchie; Alexander, Nange; Human, Domingo, Dzvukamanja; Macuphu.
Subs: Prince, Hlanti, Phillips, Mathebula, Monare, September, Doutie, Hotto, Eva Nga.