Two early goals in the first half from Luther Singh and Grant Magerman gave the hosts early promise.
But they went to sleep in the second half and the Zebras replied with two identical headers from Lebogang Ditsele and Thatayaone Ditlhokhwe who scored at the death.
Coach David Notoane was disappointed to see his team, largely made up of U23 players losing in this fashion.
Credit should go to the Zebras for their comeback and using their experience to frustrate the youthful South African team in the second half.
They will now meet Lesotho in the semi-final on Wednesday at the Moses Mabhida Stadium. Botswana caretaker coach Mogomotsi Mpote reflects on the game.
Notoane says their loss was a combination of inexperience and lack of game management especially in the second half and towards the end of the game.
They will now drop to the Plate section and face Uganda in the Plate semi-final tomorrow at the Princess Magogo stadium.
Meanwhile, Notoane has given an update on the injury that French based attacker Keagan Dolly suffered on Friday, it forced him out of this tournament and also put his African Cup of Nations (AFCON) chances in doubt.
But SABC Sport understands that the injury is not that serious but it was a precautionary measure from the medical team. – Report by Velile Mnyandu