Nigeria have appeared at all nine Women’s World Cups since the first was held in China in 1991.
Missing out is unlikely to go down well in a country where football fans are used to their team dominating, with the Super Falcons having won Wafcon a record 10 times.
But seeing off Desiree Ellis’ well-drilled Banyana team was never likely to be easy.
While the first half in Casablanca was a non-event, the second period was anything but, with chances aplenty.
Asisat Oshoala should have done better when she bundled her way through several challenges and poked goalwards from inside the six-yard box, failing to get the requisite power on her strike to trouble Swart.
The six-time African footballer of the year was subbed soon after and there will no doubt be questions about whether the 31-year-old might have appeared at her final Wafcon.
The breakthrough came on the counter in the 56th minute, with striker Ronnel Donnelly playing an exquisite through ball from midway inside her own half to set Hildah Magaia free.
Magaia’s cross from the left was met by the onrushing Kgatlana, whose shot had enough power to sneak over the line despite keeper Chiamaka Nnadozie getting a strong hand to it.
Nnadozie did keep out another Kgatlana effort five minutes later, while Swart pulled off a stunning save from Uchenna Kanu’s header, diving acrobatically to her left to palm the ball away one-handed.
Jane’s goal came courtesy of a deflection off Ucheibe’s outstretched foot in the 77th minute and Magaia should also have scored when clean through less than a minute after the restart.
It looked as if Nigeria would be unable to create a way back into the game until Jane’s unnecessary handball was spotted by the video assistant referee (VAR).
The captain did not need to stretch out her arm, with Swart well placed to save on the goalline.
With the numerical advantage, Nigeria piled on the pressure and almost found salvation in the 97th minute when Alozie drilled the ball back across goal, only to see Swart’s left boot shoot out to stop it flying into the bottom corner.
Swart and South Africa celebrated their victory with glee, but a place at the World Cup is far from certain.
They must first negotiate a six-team league alongside Ghana in November and December, with Asian sides Uzbekistan and Chinese Taipei, Papua New Guinea from Oceania and Ecuador from South America also involved.
The top two sides from that mini-league will advance to a final inter-continental qualifier in February, with three sides from that booking their spot in Brazil.