After that 2-1 loss to Sundowns last Saturday, Chiefs coach Ernst Middendorp will be delighted with the character his side have shown to bounce back.
Wits, meanwhile, have their five-game unbeaten streak brought to end and fail to extend their lead at the top of the standings with Pirates now just two points off the pace.
Kgotso Moleko replaced Godfrey Walusimbi at the back for Chiefs and Teenage Hadebe came in for Willard Katsande in midfield. Wits made just the one change with Mxolii Macuphu preferred to Lehlonolo Majoro upfront.
The hosts had more of the ball in the opening exchanges and came close to scoring as early as the third minute when Sifiso Hlanti's piledriver rose inches above the bar.
Although Wits were enjoying more possession, Amakhosi were looking dangerous on the counter-attack, with Khama Billiat looking particularly threatening. The Zimbabwean striker shot over in the 20th minute after decent build up from the visitors.
It was a battle of attrition with clear-cut chances at a premium as both teams failed to provide adequate service to their respective frontmen. The defences of both sides were coming out on top.
After an uneventful 15 or 20 minutes, the game had its first real shot in anger as Chiefs replacement goalkeeper Virgil Vries was forced in to a full-length dive in saving Terrence Dzvukamanja's sweetly struck long range effort on the the stroke of half-time.
The second half was a much more open affair. In the 58th minute the game was brought to life when Siphosakhe Ntiya-Nitiya got on the overlap and whipped in a delicious cross for Leonardo Castro to tap home at the front post for a 1-0 lead to the visitors.
Shortly afterwards, Ekstein produced a lovely cross for Lebogang Manyama, but the winger's header went narrowly wide. By now Chiefs were really in the ascendancy as Castro struck a cross-cum-shot across the face of goal that caused more concern for the Clever Boys' defence.
The points would be wrapped up in the 78th minute after excellent combination play between the Chiefs forwards. Hendrick Ekstein started and finished the move, laying off the ball to Castro who fed Parker on the overlap; the substitute cutting the ball back for Ekstein to finish.
Wits: Keet, Hlatshwayo, Mkhwanazi, Johannes, Hlanti, Monare, Alexander, Dzvukamanja, Hotto, Pelembe, Macuphu.
Subs: Goss,Mere, Mhango, Claasen, Domingo, Motupa, Majoro.
Chiefs: Vries, Cardoso, Booysen, Moleko, Hadebe, Maluleka, Ekstein, Manyama, Billiat, Ntiya-Ntiya, Castro
Subs: Bvuma, Gordinho, Walusimbi, Mahlasela, Moon, Ntshangase, Parker.