Bafana Bafana of South Africa, who shocked hosts Egypt in the previous round, had equalised with 19 minutes remaining in Cairo when Bongani Zungu headed home and the match was seemingly headed for extra-time.
After an intense VAR decision, Zungu's goal stands and Bafana level matters in Cairo.
But Troost-Ekong bundled home in the 89th-minute minute after Williams made a hash of a corner to dash South Africa's hopes of progressing and left Nigeria still chasing their dream of a fourth AFCON title.
It was a just result for a Nigeria team after they had largely dominated and led in the 27th minute through Samuel Chukwueze, who was part of a lively Nigeria front four that opened South Africa up several times
Samuel Chukwueze became the youngest scorer at the Total AFCON2019.
The opening minutes and Nigeria pressing the South Africans. Its all about the quick movement for both sides. Bafana really struggling to find space as Nigeria's back four not allowing Tau, Lorch or Mothiba to get any space.
The result extends South Africa's record of never having beaten Nigeria at the Cup of Nations, while Gernot Rohr's men moved into the last four – where Ivory Coast or Algeria await - with a disciplined, determined performance.
Nigerian President, Muhammaduu Buhari has congratulated the Super Eagles for a well deserve victory over South Africa as Nigerian men matched to semifinal adding that with two more victories, the trophy will come to Nigeria.
The President Wrote: "Congratulations to the Super Eagles on a well-deserved victory over South Africa, tonight. You represent the resilient and indomitable Nigerian spirit. Two more victories, and the coveted Trophy will come home to us. All Nigerians are looking forward eagerly.
The Super Eagles have qualified 9 times from 10 times they have played at this quarterfinal stage. Nigeria became the second team (after Senegal) to reach #TotalAFCON2019 semifinal after defeating South Africa 2-1 at the Cairo International Stadium on Wednesday night.
SAMUEL CHUKWUEZE of Nigeria has been selected as the Total Man of the Match
Nigeria XI
Akpeyi; Awaziem, Ekong, Omeruo, Collins, Ndidi, Etebo, Musa, Iwobi, Chukwueze, Ighalo.
Bafana Bafana XI
Ronwen Williams (GK), Thamsanqa Mkhize, Sifiso Hlanti, Buhle Mkhwanazi, Thulani Hlatshwayo (captain), Dean Furman, Kamohelo Mokotjo, Bongani Zungu, Thembinkosi Lorch, Percy Tau, Lebo Mothiba
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