Venezuelan striker Gustavo Paez netted the winner in the 92nd minute to ensure that Chiefs ended in the fourth position on the log.
The Amakhosi had a number of opportunities in the opening 20 minutes in particular and could’ve been 3-0 up during that period, such was their command on the game.
The main culprit for Chiefs was young forward Emmanuel Letlotlo, who wasted two excellent opportunities.
The first chance came in the seventh minute following a delightful cross from Gustavo Paez presented Letlotlo with a free header inside the box, but he somehow managed to direct the ball over the top.
Twelve minutes later, Letlotlo was put through on goal by Ryan Moon, but again the 21-year-old found the side-netting instead of hitting the target.
The third big miss for Chiefs was in the 20th minute when Hendrick Ekstein played a one-two with the classy Paez, but booted the ball wide when it seemed easier to score.
That was the story of the opening 45 minutes for Steve Komphela’s outfit, with Moon also unable to generate enough power for a shot on goal.
Wits, having already been crowned champions, seemed to just go through the paces after receiving a guard of honour from Kaizer Chiefs before kickoff.
Their only real threat in the first half was experienced midfielder Elias Pelembe, who was a constant menace on the right-hand side, but he had little support from his teammates.
To make matters worse for Gavin Hunt’s team, they lost star winger Daine Klate to what looked like an ankle injury before half-time.
The Clever Boys came out for the second half looking much sharper, though, and Vincent Pule was the man who tried to make things happen for Wits.
Pule’s pace and trickery troubled the Chiefs defence, and he had two great chances before the hour-mark, but was unable to convert.
One curler went just beyond Itumeleng Khune and the right-hand upright, while another burst of pace saw him turn Bafana right-back Ramahlwe Mphahlele inside-out, with his left-footed shot taking a deflection off Lorenzo Gordinho on to the upright.
Ekstein was becoming more influential as the game wore on, and a long-range shot in the 66th minute was tipped over the bar by Wits goalkeeper Darren Keet.
But with the game winding down and the Wits fans getting ready to celebrate the trophy presentation, Paez was set up by George Lebese to grab the winner in stoppage time.