Thulani Hlatshwayo, Sibusiso Vilakazi and Dean Furman were all on the scoresheet in Wednesday's contest as South Africa headed to the showpiece in Equatorial Guinea with a morale-boosting victory.
Bafana Bafana initially struggled to put their stamp on the game as Mali maintained possession well without troubling Jackson Mabokgwane in the South Africa goal.
South Africa went ahead somewhat against the run of play in the 37th minute when Hlatshwayo was on hand to head home Mandla Masango's free-kick.
Bongani Ndulula saw an effort cleared off the goalline just after the hour mark, but South Africa's lead was doubled in the 82nd minute when Vilakazi played a neat exchange with Andile Jali before rounding the goalkeeper and slotting into the unguarded goal.
There was further gloss to the scoreline five minutes from the end when Doncaster Rovers midfielder Furman placed home the rebound after seeing his initial shot saved.
South Africa have not lost since a 5-0 defeat to Brazil in March and Ephraim Mashaba's men will look to take that confidence into their Group C opener with Algeria on Monday.
Mali have little time to feel sorry for themselves and they start their tournament against Cameroon in Group D on Tuesday.
Watch every match of the Africa Cup of Nations LIVE on British Eurosport HD or sign up to Eurosport Player and follow the action on mobile, tablet and other devices: www.eurosportplayer.com
