The Cape Town showdown is a highlight of the 14-fixture matchday 2 schedule along with Cameroon-Ivory Coast in Yaounde and Egypt-Tunisia in Cairo.
There were doubts whether the Nigeria game would go ahead, but controversially-elected national football federation boss Chris Giwa stepped aside to prevent a worldwide FIFA ban.
African governing body CAF had warned Nigeria that failure to play in South Africa would have resulted in disqualification from the competition.
Reigning African champions Nigeria have won five and drawn one of six matches against South Africa in the World Cup and Cup of Nations.
Not only have Bafana Bafana (The Boys) failed to defeat the Super Eagles, they have not scored even one goal.
The countries made contrasting Group A debuts last weekend with South Africa winning 3-0 in Sudan while Nigeria were stunned 3-2 by visiting Congo Brazzaville.
It was a dream start for new South Africa coach Ephraim ‘Shakes’ Mashaba and a young, much-changed side with Sibusiso Vilakazi scoring twice in the stamina-sapping Omdurman heat.
Nigeria surrendered a 46-match unbeaten home record in Cup of Nations qualifiers and looked a shadow of the team that overcame Burkina Faso 1-0 in the 2013 final to win a third African title.
Mashaba says he has a “gut feel” that South Africa can end the 22-year dominance of Nigeria.
“Wednesday could be a defining moment — it is time to kick this habit of losing to Nigeria,” stressed the 64-year-old promoted last month from national youth team coach.
“Bafana have become a laughing stock and our duty is to restore pride in the national team. Winning in Sudan was the start of a rebuilding process.”
South African Footballer of the Year Vilakazi said the attitude of the players had changed dramatically since Mashaba succeeded sacked Gordon Igesund.
“They are prepared to fight and want to bring pride and happiness to the country. We are aware of our record against Nigeria and need to change it.”
Nigeria caretaker coach Stephen Keshi blamed the Congo defeat on a lack of aggression, playing to the crowd, and slowness to the ball.
“I was more upset by the way we played than the result. We scored first and thought it would be easy,” said the 52-year-old handler known as ‘Big Boss’.
“Even when we fell two goals behind, there were enough scoring chances to draw at least. Now we must go to South Africa and win.”
A change Keshi may consider is starting with burly Turkey-based striker Emmanuel Emenike, who troubled Congo when he came off the bench for the second half.
The Nigerian defeat in Calabar means Cameroon are the only team never to lose a home Cup of Nations qualifier.
A new side without retired striker Samuel Eto’o and suspended midfielder Alex Song started their Group D campaign with a 2-0 away win over a lack-lustre Democratic Republic of Congo.
Ivory Coast came from behind at home to edge Sierra Leone 2-1 through goals from recalled Seydou Doumbia and Gervinho to give French coach Herve Renard a winning start.
“We lacked speed and width at times,” admitted Renard, who steered outsiders Zambia to the 2012 African title with a penalty-shootout win over Ivory Coast.
“I believe we will do much better in Yaounde,” he said of a match between two countries eliminated after the first round of the 2014 World Cup in Brazil.
Record seven-time African champions Egypt were lucky to lose only 2-0 in Senegal as Group G unfolded and Tunisia looked largely unimpressive when winning 2-1 at home to Botswana.
Egypt dare not lose against Tunisia in Cairo if they want to avoid the humiliation of failing to qualify for a third consecutive tournament having won the previous three.
Algeria, the most impressive African team at the World Cup, host Mali and Ghana are away to Togo in other attractive pairings.