Nigeria went into the game with a perfect Nations Cup record against South Africa, having beaten Bafana Bafana in all three of their previous meetings in the competition including a semi-final meeting in 2000 in Lagos.
But despite being urged on by the cacophonous horn section carried by the supporters in green and white, Jose Peseiro’s side failed to live up their billing as favourites in a ponderous first half which South Africa largely bossed.
Forward Percy Tau had their best chance, scuffing his shot straight at Nwabali when unmarked inside the penalty area.
Nigeria’s lack of potency was reflected in the statistics, with African Footballer of the Year Osimhen only managing nine touches in the half, including a header which went wide just before the break.
But things then livened up notably as Nigeria came out with greater intent in the second half.
Osimhen put one of several presentable headed opportunities over the bar before Frank Onyeka blazed wastefully wide.
The Super Eagles finally broke the deadlock in the 67th minute when Osimhen’s driving run was abruptly ended inside the penalty area by a poor challenge from defender Mothobi Mvala.
As in the group stage win against Ivory Coast, it was captain Troost-Ekong who assumed penalty duties rather than Osimhen.
And the former Watford defender sent his effort down the middle and under the legs of Ronwen Williams, the shootout hero for South Africa in the quarter-final win over Cape Verde, as the goalkeeper dived to his left.
After Evidence Makgopa had fizzed a skimming effort just wide for South Africa, Ademola Lookman should have won it for Nigeria but hesitated when trying to round Williams, allowing the keeper to dive at his feet and gather the ball.
Late VAR drama denies Osimhen
With just five minutes of normal time remaining, Osimhen thought he had clinched victory, turning home Bright Osayi-Samuel’s low cross following a swift counter-attack and sprinting towards the Nigeria fans for a celebration that was short-lived.
South Africa’s players were already protesting before referee Amin Omar was advised to go to the monitor by the video assistant referee, with the Egyptian quickly ruling out Osimhen’s strike and, in yet another late twist at this remarkable tournament, pointing to the spot at the other end for an earlier foul on Tau by Alhassan Yusuf.
Mokoena kept his calm to convert the penalty and deny Nigeria five consecutive clean sheets – and South Africa should have won it in the six minutes of added time when Khuliso Mudau only succeeded in blazing over after Nwabali parried Mokoena’s free-kick into his path.
Williams saved efforts from Lookman and Osimhen early in extra time but the best opening came when Terem Moffi latched on to a through ball and ran powerfully towards the South Africa goal.
But Kekana stopped the substitute’s run with a trip and, following a VAR review, was shown a straight red card and Nigeria were awarded a free-kick just outside the area.
Iheanacho drew a save from Williams from the set piece but decided the shootout after Nwabali had saved from Mokoena and Makgopa, with the Bafana Bafana captain unable to repeat his heroics from the last eight.
