Buhle Mkhwanazi's own goal put the Super Eagles ahead in the 10th minute before Lebo Mothiba's equaliser six minutes later.
Despite two questionable offside calls costing Gernot Rohr's men two goals, they remain at the summit of Group E with 10 points from five matches and will return to the Afcon stage for the first time since 2013.
And football enthusiasts on social media have showered praise on the team for their performance and feat.
South Africa 1 - 1 Nigeria. I'd take that. Nigeria has qualified for the next AFCON. Welcome back Super Eagles!— JJ. Omojuwa (@Omojuwa) November 17, 2018
We qualified.... good job Super Eagles 🇳🇬 #RSANGA— Do2dtun Energy gad (@iamDo2dtun) November 17, 2018
BREAKING: The Super Eagles 🦅 of Nigeria qualifies for the Nation’s Cup.— Adeyanju Deji 🇳🇬 (@adeyanjudeji) November 17, 2018
Q U A L I F I E D pic.twitter.com/SQydTbHFvS— Soar Super Eagles 🦅 (@SoarSuperEagles) November 17, 2018
Congratulations super eagles qualified for Cameron 2020 afcon pic.twitter.com/Wa2NVZNASS— OBIM OKOYE. 🇳🇬🇳🇬 (@obinnaokoye18) November 17, 2018
Congratulation to the Super Eagles for returning to the top stage of African Elite football Competition after missing out on two back to back tournament 💃📈 #Team9jaStrong #SoarSuperEagles #RSANGA #AFCON2019Q pic.twitter.com/ietHimaxd9— Owoyomi Bamikole A. (@Mr__Bankky) November 17, 2018