In the absence of Fortune Makaringe through suspension, it was down to Paseka Mako to step up and continue the astounding job done by his club mate.
Bafana got off to a sluggish start as they struggled to penetrate the opposing defence who kept a firm high-line.
With no problems filtering through from the visitors, the first opportunity fell to the home side but Ryan Moon was unable to finish off.
The Kaizer Chiefs forward turned provider to Siphesihle Ndlovu, who made a late run into the box, but he too failed to finish off a perfectly-placed knockdown on 18 minutes.
Two-goal hero against Namibia, Lebogang Maboe found space on the edge of the box but his effort only found the top of the side-netting on the half-hour mark.
Moon was presented with another opportunity but his effort from an acute angle was punched away for a corner.
The resultant set-piece was taken short and Aubrey Modiba provided a cross from the right, which fell to Motjeka Madisha to head in the opener just before halftime.
Botswana gave a scare as early as the second minute into the restart when Sipho Sakane’s header flew narrowly across the face of goal..
Bafana eventually capitalised with a counterattack initiated by Maboe and calmly finished off by Modiba 12 minutes to go.
The victory was confirmed with three minutes remaining after Maboe latched onto a loose ball before racing at goal to round the keeper for a comfortable finish.
Bafana: Pieterse , Xulu , Madisha, Ngezana, Modiba, Mako, Meyiwa, Ndlovu, Links, Maboe, Moon.
Subs: Bvuma, Kubheka , Fielies, Webber, Mosiatlhaga, Foster, Singh.
Botswana: Masule, Maikano, Ramoraka, Keredilwe, Kebue, Sosome, Baruti, Modingwane, Makgantai, KSeakanyeng, Phiri.