After taking the lead through a Motjeka Madisha penalty on the 72nd minute, some goalkeeping blunders by the otherwise reliable goalkeeper Dumisani Msibi allowed Mali to come back into the match through a double strike by substitute Hamidu Traore.
It was a painful defeat for Amajita who going into this tournament, a lot was expected of them.
Scorching heat almost made constructive play impossible in the opening 45 minutes but it was the Malians who made the early running.
Amajita’s Ayabulela Magqwaka gave away position in the fifth minute but fortunately saw Malick Toure’s effort going horribly over the bar as Mali sent some warning shots.
The same player again blasted the ball wide two minutes later as South Africa’s defence continued to leave gaping holes at the back.
Typical of West Africans, the Malians used their physical strength in the opening minutes to impose themselves on the ball.
With the temperatures hovering around 40 degrees C, both teams started to give away possession, as opening clear-cut chances became a rarity.
Maraisane then got a nasty challenge from Maiga, which required him to receive some medical attention, as Libyan referee Mohamed Omara continued to flash yellow cards.
On the 37th minute, Madisha’s header from the corner kick went wide as South Africa started to fashion some chances.
Zuma’s shot on the 40th minute was too weak to trouble the Malian keeper as the relentless heat threatened to spoil the party.
Mali were the first to get a corner kick in the second half and moments later Msibi was beaten to the ball but captain Ichaka Diarra’s header went narrowly wide as Amajita breathed a sigh of relief.
Amajita were again caught with numbers on the break in the 53rd minute but captain Madisha saved the situation.
Tlotlo Leepile then came in for Pule Maraisane who apart from carrying a head injury and a yellow card, was not at his usual best. Tshidiso Monamodi also came for injured Haashim Domingo.
Madisha then put South Africa ahead on the 72nd minute after Dumisani Zuma was brought down in the box to make it 1-0.
Mali made it 1-1 through a long range looping shot by substitute Hamidu Traore although, Msibi could have done better.
Mali then took the lead (2-1) in the 86th minute through Traore who again took advantage of indecisiveness of Msibi in goals.
If Ghana draw with Zambia or beat them in the later game, South Africa will have been knocked out of the tournament.
Amajita starting 11: Dumsani Msibi (GK), Kabelo Seriba, Tebogo Moerane, Motjeka Madisha (c), Ayabulela Magqwaka, Morne Nel, Siphelele Luthuli, Moegammad Domingo, Pule Maraisane, Thami Masiya, Dumisani Zuma
Mali starting 11: Sory Traore, Ichaka Diarra, Hamidou Maiga, Aboubacar Doumbia, Falaye Sacko, Alassane Diallo, Malick Toure, Mohamed Guilavogui, Souleymane Diarra, Youssouf Kone, Saliou Guindo.