Mali overcame South Africa with two quick-fire goals in the second half from Hamari Traore and Lassine Sinayoko.
The Eagles were dominant in possession throughout the first half but it was Bafana Bafana who should have opened the scoring.
Percy Tau had a glorious opportunity as South Africa were awarded a penalty after Niakate elbowed Makgopa in the face inside the penalty area. After a swift VAR check, a penalty was awarded and up stepped Tau.
The 29-year-old blasted over the bar, much to the delight of Mali fans in the crowd. The former Brighton & Hove Albion striker had multiple chances to make amends following the missed penalty but his finishing lacked composure and ultimately that was what cost his side the victory.
South Africa should take optimism from this match as they played well for the majority of the game but fell apart in the second half.
Following Sekou Koita's free-kick that hit the bar, Traore followed up well and tapped home.
Mali then quickly struck again, this time through Sinayoko who burst into the box, shrugged off a defender and calmly slotted past Ronwen Williams.
The Eagles will go up against Tunisia at the weekend in the second match of Group E and South Africa will face Namibia.
AFCON results, scores, group tables
Hosts Ivory Coast will kickoff the opening fixture against Guinea-Bissau on January 13 in Abidjan.
The Round of 16 starts on January 27, with the quarterfinal and semifinals beginning on February 2 and 7 respectively.
FT: That's all! Mali get the win after a quick-fire double in the second half put the game to bed. South Africa really could have been ahead on multiple occasions in the first half and will be kicking themselves for not doing so.
⌚ FULL-TIME!
A strong second half display