South Africa survived a few scares early on and goalkeeper Mondli Mpoto needed Reeve Frosler to be on hand to bail him out after he was late to get back onto this line.
Mpoto had another nervy moment just minutes after that and was relieved to see Mali flagged offside after a dangerous attempted sweep-up at the back.
It was a physical first half with Amajimbos handling aerial balls well but Mali keeping up the pressure.
Amajimbos absorbed the pressure from Mali and managed to created some good situations on the break in an evenly matched tie with both defenses standing firm.
But after a period of sustained pressure at the start of the second half, Mali eventually took the lead through Siaka Bagayoko in the 65th minute following some poor marking at a corner.
Mpoto had made a number of saves to keep South Africa in the game, with one particularly impressive, while the Malians also missed several chances with shots that went wide.
It was game over in the 78th minute when Aly Malle doubled Mali's lead with 12 minutes remaining, getting just reward for another sustained period of pressure to inflict the killer blow with a curling that gave Mpoto no chance.
The Malians showed superior physical dominance and endurance to get the second goal towards the end of the match as Amajimbos ran out of ideas.
South Africa had a Khanyiso Mayo goal ruled out for offside in the 88th minute following good work by the lively Sibongakonke Mbatha and never gave up after a spirited performance, as they kept on pushing to the end.
Amajimbos end as runners-up, while Guinea claimed third place earlier on Sunday after beating Nigeria 3-1 in the third-place playoff.
Coach Molefi Nseki will be proud of his side's achievements and will now turn his attention to preparing the team to compete at the FIFA Under-17 World Cup.
Amajimbos XI: Mpoto, Ngcobo, Frosler, Mohamme, Mukumela, Dlala, Meyiwa, Maluleke (c), Mbatha, Mkatshana, Mayo
Mali XI: Traore, Dante, Bagayoko, Sangare, I Traore, Mamadou Fofana, Koita, Malle, Maiga, B Traore