Elias Pelembe replaced the suspended Deon Hotto as Phathutshedzo Nange also made a return to the Clever Boys side that edged Black Leopards in the Absa Premiership on Tuesday.
Wits almost got the opener after five minutes when Terrence Dzvukamanja slipped in a through ball from Bienvenu Eva Nga, but the home side scurried to clear off the line while Kings had to wait until the half-hour mark for a chance when Sedwyn George brought the best out of Brandon Petersen who produced an acrobatic keep out the former's first-time volley.
The visitors regrouped afterwards as Dzvukamanja fired into the side-netting after a pass from Sifiso Hlanti on the left side of the area.
The Clever Boys finally had the upper hand when Eva Nga got ahead of Zitha Macheke's cross to head into the bottom corner two minutes to halftime.
Lorenzo Gordinho rubbed further salt in the home side's wound five minutes after the halftime brak after getting on the end of Pelembe's corner to nod home at the far post.
A third goal came three minutes later when Lesego Manganyi helped Dzvukamanja's rasping shot from the right side past Sabelo Nkomo.
Levy Mashiane went close to bringing the tally down with a low drive before the 60th minute, but Petersen got ahead of the strike to parry for a corner kick.
Dzvukamanja finally edged his name on the scoreboard after running onto Pelembe's through ball to round Nkomo for an easy finish eight minutes later.
Hlanti soon made way for the Clever Boys in the final quarter as Keegan Rtichie replaced the Bafana Bafana international, but Wits were in the clear of any danger late on to secure a spot in the semi-final.