This was the first of two matches scheduled for the trip to Botswana in preparation for the 2015 African Youth Championships (AYC) qualifier against Tanzania on July 18.
The second match, a full international, will be played on Sunday at the Molepolle Stadium.
South Africa started brightly in the first half and did not look like a team that was playing its first match in 2014.
Midfielder and captain Nelson Maluleka should have opened the scoring as early as the eighth minute, but ballooned his shot with the keeper to beat.
In the 13th minute striker Vuyo Mkatshana went one-on-one with the Botswana keeper but his first touch let him down. But a minute later he made amends and scored from a cross to give the visitors a 1-0 lead.
The hosts came back strongly in the second half and dominated proceedings.
Seven minutes into the second stanza, South African goalie Mxolisi Skei misjudged the ball, which fell into the path of Tshepo Malgase, but he shot over when scoring appeared easier.
The visitors could have increased their lead when second half substitute Benedict Matlawe found himself in good space in the area, but he pushed the ball too hard which was easily dealt with by the keeper.
Botswana almost found an equaliser in the 65th minute with the South African defence in trouble, but Malgase again ballooned his shot.
In the 77th minute the hosts bridged the Amajimbos defence but substitute Kgothatso Thobane could not get past Skei, who blocked the ball with his legs for a corner.
Despite playing under pressure in the second half, the visitors were the ones who got a goal five minutes from the final whistle with a free-kick by defender Kananelo Motsoeneng after a foul on Charles Baloyi.
Botswana: Thomas Manyelela , Benjamin Dikagiso, Kgosietsile Ernest, Godfrey Sebolai, Kabelo Letshola, Lebogang Powell Lekgethiso, Tshepho Malgase, Jonathan Ntagileng, Takongwa Tafa, Thatayaone Ditlhokwe (c), Karabo Sebeo
South Africa: Mxolisi Skei, Simon Nqoi, Thendo Mukumela, Katlego Mohamme (Keanu Cupido ‘63), Kananelo Motsoeneng, Samuel Nkomo (Thato Pheleu ‘63), Vuyo Mantjie (Charles Baloyi ‘63), Sibongankonke Mbatha, Vuyo Mkatshana (Edwin Sekwama ‘63), Nelson Maluleka (c), Felix Noge (Benedict Matlawe ‘63)