Kaizer Chiefs came into this league encounter looking to finish top of the Q-3 log and they dictated the pace of the game immediately after kick-off, but they were unable to break the Mpumalanga Black Aces' defence.
George Lebese's shot from the edge of the box, took a huge deflection for AmaKhosi's corner as the home side continued to put their opponents under immense pressure in the early stages of the game.
Lebese was again afforded space outside the box and this time the Chiefs' winger hit the target although it went straight into Jackson Mabokgwane's hands.
Aces didn't threaten the defending champions in the opening 28 minutes of the game, and they nearly went behind in the 22nd minute when Chiefs won a free-kick outside the box. However, Bernard Parker's attempt was brilliantly saved by Mabokgwane.
AmaZayoni should have punished Chiefs in the 29th minute after a delightful cross was played to Tendai Ndoro by Abia Nale, but the lanky striker placed his chance wide of Khune's goal.
Parker's header from Siphiwe Tshabalala's ball went over the bar in the last five minutes of the first half as AmaKhosi restricted movement from any of the Aces' players inside the box including their goalkeeper Mabokgwane.
The visitors had their penalty appeal turned down just before the interval after Ndoro was clearly brought down by Willard Katsande inside the box, but none of the two teams could break the deadlock going into the second half.
Chiefs looked for an early second half goal, but Nkhatha was unlucky to have not hit the target with his header, coming just after the restart following a beautiful free-kick played into the penalty area by Parker.
Ndoro raced onto Mabizela's lob behind the Chiefs' defence toward the hour-mark, but Itumeleng Khune came off his line to arrive first on the ball to make a clearance.
Parker wasted a glorious chance to put AmaKhosi in front in the 62nd minute, as he failed to give his volley enough power to beat Mabokgwane, who positioned himself well to make a routine save.
Parker was again guilty of wasting another clear-cut chance after he failed to turn in Katlego Mphela's 73rd minute cross home from close range.
Aces almost got punished in the 83rd minute, but Katsande missed the target as his header went inches wide with Mabokgwane well beaten.
The visitors broke the deadlock deep in stoppage time when Nale played substitute Miguel Timm through, and the Aces midfielder slotted past Khune to give AmaZayoni another memorable victory in Soweto.