After 90 minutes without a goal, Moeketsi Sekola scored three minutes into the additional time, with Sthembiso Dlamini on target just two minutes later, before Danny Venter added a third with 111 minutes on the clock.
Daine Klate netted a very late consolation goal for the out-of-sorts Clever Boys a minute before the final whistle.
It was a tough blow to take for the MTN8 champions, with Hunt insisting his side should have been ahead in the first half, before praising Ea Lla Koto for being the better side on the day.
And while Wits missed a number of chances, there was also a strong call for Bokang Tlhone to be dismissed for a heavy challenge on Thabang Monare which led to his substitution.
Hunt told SuperSport: "Disappointed, firstly, with the result and I was disappointed with the performance.
"I thought in the first half of the game we should have been out of sight – it should have been 4-0, 5-0; they should have had a red card in the first half.
"A blatant red card (but) we didn't get it (in our favour), so things went against us and we came and battled away. The first shot they had at goal, they scored and again from the next shot.
"At the end of the day, you look at the scoreline, you can say we were well beaten, but to be fair we weren't at our best," he added.
"We've got to give them credit - they pressed and they kicked the 'Sugar Honey Iced Tea' out of us, which is what it's all about, and if you don't stand up to it...
"We didn't match it and we didn't play football today, but you've got to give them credit and well done to them.
"Certainly, from our side, the chances we missed were schoolboy errors and, obviously, the longer it went on the better they got."