It was a frustrating afternoon for the Pretoria side, who had most of the play, but struggled to make their chances count.
They conceded just before the break, but fought back with an injury-time equaliser, only for a goalkeeping blunder to put AmaZulu back in front.
Dario Monteiro then forced the match into penalties, but a superb showing by AmaZulu keeper Mbongeni Mzimela ensured the KZN side remains on track for cup honours.
AmaZulu buried the first real chance that came their way; Dumisani Ngwenya smashing the ball past Dennis Onyango following Thabo September’s slip-up in defence.
Prior to the goal, neither keeper had been overly extended as chances remained scarce in an evenly balanced match.
Ngwenya did, however, have a half-chance just seconds after the kick-off when he raced onto Warren Bishop’s long ball, but his attempted lob cleared the bar.
Brent Carelse then dragged a shot just wide for Matsatsantsa, while Tebogo Langerman’s breath-taking run only lead to a corner when a goal seemed on the cards.
SuperSport came flying out of the blocks in the second half as they searched out an equalizer, and it nearly materialised in the 51st minute, but Mzimela made an excellent stop from Petrus Mahlatsi’s drive.
United again came close in the 73rd minute, but Mzimela denied Gavin Hunt’s team a goal as he made a good near-post save from Brian Umony’s shot.
For Usuthu it became a case of hanging on for dear life as Laffor’s shot was deflected wide and then Mzimela made a sensational stop to clear Monteiro’s shot off the line in the 82nd minute.
AmaZulu looked to have the win in the bag, but a brilliant 92nd-minute free-kick from Carelse ensured the game went into extra-time.
Usuthu nearly conceded a second goal just after the start of extra-time, but somehow Hlompho Kekana’s shot was kept out of the net.
They were then handed a real gift in the 96th minute as Onyango let Marc van Heerden’s free-kick slip through his hands and into the back of the net.
Van Heerden nearly scored a 105th minute own-goal when his header hit his own crossbar, and 10 minutes later the home team levelled matters at 2-2 when Monteiro scored with a well-taken header.
Having fought back twice to force the game into penalties, the home team capitulated at the final hurdle as Monteiro and Carelse had their spot-kicks saved.