Both regular-time goals also came from penalties with captain William Troost-Ekong scoring after 67 minutes for Nigeria and Teboho Mokoena equalised from a 90th-minute spot-kick.
The Mokoena equaliser came after Nigeria thought they had scored a second goal through a tap-in from star forward Victor Osimhen.
But play was called back to the other end of the field after VAR alerted the Egyptian referee that South African Percy Tau had been fouled in the area, and the match official concurred.
Khuliso Mudau had a chance to win the South Africa in added time at the end of regular time, but blazed over after goalkeeper Stanley Nwabali parried a Mokoena free kick.
South Africa finished with 10 men when Grant Kekana was sent off on 115 minutes for a last-defender foul.
Nigeria entered the match with a perfect record against South Africa in the premier African football competition having won three previous meetings.
The Super Eagles beat Bafana Bafana (The Boys) 2-0 in a 2000 semi-final in Nigeria, 4-0 in a group match four years later in Tunisia and 2-1 in a 2019 quarter-final in Egypt.
Nigeria coach Jose Peseiro made one change to the team that beat Angola 1-0, bringing in Bright Osayi-Samuel for left-back Zaidu Sanusi, who did not train on the eve of the match.
Star Napoli forward Osimhen started for the three-time champions after recovering from an abdominal discomfort that delayed his arrival in Bouake from Abidjan.
(Vanguard)
