More than 16,000 were in attendance at the Amadou Gon Coulibaly Stadium in Korhogo to see whether South Africa could spring another surprise in a stadium and a group where Namibia had shocked Tunisia 1-0 earlier in the day.
But Bafana Bafana's best chance to cause such an upset was squandered midway through the first half when ex-Brighton forward Percy Tau stepped up to take a penalty awarded by VAR. He skied the ball high over the crossbar, and the contest was still goalless at the interval.
After the break, Mali turned the screw and took the lead on 60 minutes when Kamory Doumbia’s free-kick slammed the underside of the crossbar. Skipper Hamari Traore tapped home from on the line.
It took just six minutes for Mali to double their lead, with Lassine Sinayoko outmuscling Siyanda Xulu and calmly slotting under goalkeeper Ronwen Williams.
That quickfire double proved enough for Les Aigles, who go top of Group E after a fully merited victory.