The capital side took the lead early in the first half, but Chiefs hit back with goals from Reneilwe Letsholonyane and Willard Katsande to move up to third on the log standings.
With both Maritzburg United and Jomo Cosmos picking up points, it remains very tight at the bottom of the league standings with two points separating the three relegation contenders.
Chiefs, though, have been fighting their own battle and registered a shot on target with 10 seconds on the clock. Siphiwe Tshabalala forcing Tristyn Coetsee into a straightforward save.
For all their defensive frailties this season, AmaTuks have been transformed in attack since Shaun Bartlett's arrival and took the lead on five minutes.
Vuyisile Ntombayithethi pounced on the loose ball to drive a powerful shot into the back of the net via the inside of the post, 1-0 to the hosts.
The AmaTuks midfielder had Khune scrambling once again in the 24th minute - lucky for the goalkeeper the his rocket flew just wide.
Chiefs kicked into gear soon after - creating chance after chance with no end product. Bernard Parker found acres of space in the penalty area, but failed to hit the target before George Lebese saw his shot sail just over the crossbar moments later.
The visitors continued to turn the screw after the break, but came up against a determined Coetsee who kept his cool to gather the ball at Parker's feet before the hour mark.
Chiefs, though, finally found their goal through second-half substitute Letsholonyane. The midfielder tapping in from close range after Coetsee could only manage to parry a close range shot in the 72nd minute.
Steve Komphela's men continued to dominate and scored the winner in the 85th minute. Katsande heading home at the back post after AmaTuks failed to clear from a corner-kick.
The win is Chiefs' first in the league since February.