The result was enough to see the South Africans finish top of the pool with seven points following two wins and a draw.
Banyana will face Zambia, who topped Group A, in the first semi-final on Thursday.
Tournament hosts Zimbabwe will have to wait 24 hours to learn their fate after being held to a 3-3 draw by Malawi – a result which left the home team in second place in their group.
Zimbabwe have five points from their three matches and must now wait to see what happens in the Group B clash between Kenya and Swaziland on Monday. A Swaziland win will take them and the Kenyans through to the semi-finals, but a draw or a Kenyan win will see Zimbabwe advance as the best-placed runner-up.
Banyana made changes to the squad that defeated Namibia, but the move seemed to backfire as they gave a lacklustre performance.
It was Botswana who looked more organised and kept the South African defence busy.
After a disappointing first half, Banyana interim head coach Desiree Ellis introduced strikers Chantelle Esau and Thembi Kgatlana, in place of Nwabisa Kolisi and Koketso Tlailane.
The change seemed to bring life back to the South African side – but it was Botswana who stunned everyone with a goal in the 83rd minute following a defensive blunder by another substitute Nothando Vilakazi, who instead of clearing the ball was undecided and Tholakele of Botswana pounced and scored to give her side the lead.
But the lead was short-lived as Esau grabbed an equaliser just four minutes later to earn a share of the spoils.
It was Esau’s third goal in three matches. She is on par with Kgatlana.
Yolula Tsawe (GK), Noko Matlou, Zanele Nhlapo, Bambanani Mbane, Koketso Tlailane (Thembi Kgatlana), Nkoikoi Mabina (Nothando Vilakazi), Refiloe Jane (C), Nompumelelo Nyandeni, Rachel Sebati, Nwabisa Kolisi (Chantelle Esau), Rhoda Mulaudzi
Roxanne Barker (GK), Andile Dlamini (GK), Lebohang Ramalepe, Nothando Vilakazi, Regina Mogolola, Kholosa Biyana, Leandra Smeda, Thembi Kgatlana, Chantelle Esau