Former Kaizer Chiefs transfer target Victor Letsoalo thrust South Africa ahead after 12 minutes following some impressive interchanges at Loftus Versfeld on Sunday.
The TS Galaxy star then turned provider with three minutes to go for captain Neo Maema, the Mamelodi Sundowns playmaker, to finish and hand Bafana Bafana a 2-0 lead.
It was a crucial victory by Molefi Ntseki's side, who had suffered a 1-0 defeat in the first leg of this African Nations Championship qualifier away.
They have now qualified for the Chan tournament to be jointly hosted by Kenya, Tanzania and Uganda in August.