The goals were scored by Lebogang Mokoena for Downs 74th minute and Sandile Gumede got the equaliser in the 89th minute to take the game to extra-time.
Usuthu had the better of first half exchanges, looking more threatening and energetic in attack.
Sundowns did have their fair share of ball possession, but their forays into the AmaZulu half were often over-elaborated, with too many passes enabling the make-shift Usuthu defence to snuff out any potential danger.
It was Ngwenya’s 32nd minute headed flick which should have lead to the opening goal as Dlamini’s pace forced Baloyi into a foul with the result that a penalty was awarded.
However, the KZN side were unable to profit from the spot kick as Baloyi saved from Tsweu Mokoro, who then blasted the rebound over the bar.
AmaZulu defender Siphiwe Mkonza had a decent chance eight minutes after the break, but was unable to react quickly enough to keep his close range shot on target.
Sundowns though began to find their rhythm, looking increasingly purposeful in attack and dominating ball possession, while AmaZulu lacked the same energy they had shown in the first 45 minutes.
Mokoena though should have out Downs ahead in the 56th minute when set up by Vilakazi, but he sent an angled shot across the goal-mouth.
The Pretoria side remained patient though, continuing to pass the ball around while probing for gaps.
And their persistence finally paid off in the 74th minute when Mokoena was put through on goal, doing the business with a delicate chip over Gindre and into goal off the underside of the goal.
Abdullah Ishaka looked to try and muster an immediate reply for Neil Tovey’s men, but his cracking long range drive was kept out by Baloyi.
Thabo Mabaso, Siboniso Gumede and Thami Sangweni also had opportunities, but they were only half chances and Baloyi was not called into action.
However, AmaZulu were not going to go down without a fight and they scored a dramatic 90th minute equaliser when Sandile Gumede headed home from close range after Downs were unable to deal with Mkhonza’s long throw-in, sending the game into extra time.
The Durban team survived an early scare in extra time when Mathew Pattison’s long range free kick crashed against the bar.
Apart from that though, it was Usuthu who were more threatening in extra time, although they were not able to create any clear-cut chances.
With both teams tiring from their efforts, a penalty shoot-out looked the only way to settle the tie.
Gindre gave AmaZulu the immediate advantage when he saved from Pattison, but Mkhonza restored parity when he blasted over.
Mokoena and Ishaka both slotted their efforts away before Gindre again put AmaZulu in front when he stopped Luvhengo Mungomeni’s effort.
Sandile Gumede and James Mayinga put their penalties into the back of net, leaving Mokoro to keep AmaZulu’s advantage in tact.
But it was not to be his side as his kick struck the upright.
Still the drama continued though – after Vuyo Mere and Dlamini both scored, Gindre again saved, this time from Vilakazi.
It was left to Litha Ngxabi to seal the game for Usuthu, and he did so, sending the ball past Baloyi’s outstretched hands.
AmaZulu: (4-4-2): Gindre, Biyela, Mkhonza, Chintu (Siboniso Gumede 46’), Ishaka; Mabaso, Sangweni, Sikhakane (Ngxabi 74’), Mokoro; Ngwenya (Sandile Gumede 80’), Dlamini.
Sundowns: (4-4-): Baloyi; Mere, Xulu, Mungomeni, Mayinga; Mmotong, Nyandoro (Ncaca 112’), Pattison, Mokoena; Vilakazi, Katongo (Phala 67’)