New Orlando Pirates signing Monnapule Saleng was handed a start on the right along with TS Galaxy starlet Ethan Brooks, while SuperSport United's Thatayaone Ditlhokwe started for Botswana.
Bafana enjoyed a lot of the ball early stages with Brooks and Sithebe dictating the pace of play in the middle of the park, clear-cut chances were hard to come by in the opening 20 minutes.
Botswana were happy to absorb the pressure and catch Bafana on the counter and that's exactly what they did on 30 minutes, but Veli Mothwa was on hand to produce a fine save to keep out Segolame Boy's strike.
Bafana started to turn up the pressure in the latter parts of the half in search of the opening goal, but they could only register a couple wayward efforts in the final five minutes.
Botswana came out firing in the second half and went agonisingly close to taking the lead on 65 minute when Thatayaone Kgamanyane rattled the crossbar with a volley from 12-yards out.
Bafana went on to take the lead two minutes later at the other as Kagiso Malinga unleashed a volley from a tight angle that caught the Botswana shot-stopper by surprise.
The South Africans were able to see out the remaining stages of the second half, but the one was not enough to take the side top of Group A after Eswatini's 3-1 win over Lesotho.
Bafana will switch focus to Thursday's encounter against Eswatini while Botswana will do battle with Lesotho.
Bafana: Mothwa, Mobbie, De Reuck, Sibanyoni, Saleng, Sithebe, Brooks, Mphahlele, Mkhulise, Phohlongo, Dube.
Subs: Vyver, Ngcobo, Ngobeni, Maart, Sekgota, Malinga.
Botswana: Morake, Leinanyane, Gaolaolwe, Ditlhokwe, Johnson, Mohutsiwa, Mpolokang, Boy, Elias, Setsile, Kgamanyane.
Subs: Malapela, Mangolo, Kebue, Thulare, Gaogangwe, Modingwane, Kgoma