Leading marksman Ibrahima Keita netted a first half brace before substitute Issa Sarr sealed victory in the dying embers of the game. In between, Phumlani Ntshangase grabbed a consolation for the South Africans.
On 16 minutes, Sarr was felled by South Africa captain Kwandakwensizwa Mngonyama for a penalty which was nicely converted by Keita for the opener.
Four minutes later, the pair teamed up again with Sarr squaring Keita, who trapped before slotting past South African goalie Stuart Goss.
The South Africans pulled one back on 28 minutes from the spot after hard-pressed Senegal defender Ibrahima Diedhiou brought down Phakamani Mahlambi. Ntshangase stepped up with an effort past Senegal goalie Pape Ndiaye.