Fargie Lakay was the hero for the home side with two first half goals to see the team through.
Cameroon took the lead in the third minute when Noubissi Marius’ low shot gave Jethren Barr no chance. Barr looked jittery in the opening minutes and could have been punished further moments later.
Pierre Kunde then saw his powerful shot fly over the bar as the visitors upped the ante.
Amajita had to again defend in numbers in the 25th minute as Cameroon threatened, but a timely tackle by captain Ayabulela Maqwaka saved the situation.
Siyanda Ngubo then saw his shot blocked inside the box as Amajita pushed men up-front searching for the equaliser.
They finally got the equaliser seven minutes before half-time when Lakay went on a solo run before burying a thunderous shot into the roof of the net.
Moments later Ngubo could have given Amajita the lead, but he decided to pass the ball inside the box when taking a shot could have been a better option.
Cameroon then hit the crossbar on a sweeping counter-attack through Tabekou Ouambe, before Lakay got a second in the dying minutes of the half to give the home team a 2-1 advantage.
The second half began at the same frantic pace as the first half with Cameroon looking to quickly hit back. But they were pegged back as Amajita hit the bar from a free-kick soon after through Lakay.
Pule Maraisane then saw his chip tantalising over the bar after being set up by Ngubo.
A few nervy moments towards the end ensued, but in the end Amajita hung on for a famous win and will now head to the tournament in Senegal.
South Africa: Jethren Barr, Madisha Motjeka, Bongane Mathabela, Ayabulela Maqwaka, Siyanda Ngubo, Pule Maraisane, Aubrey Maphosa, Denwin Farmer, Fagrie Lakay, Tshepo Chaine, Morne Nel
Cameroon: Joseph Ebogo, Bana Moussa, Thomas Libih, Pierre Kunde, Tabekou Ouambe, Christian Bassogo, Tah Anunga, Andoulo Serge, Noubissi Marius, Jean Abanda Koa, Franck Bagnack