The other two goals came from midfielders Thendo Mukumela and Sibongakonke Mbatha.
This was the second match in a week between the two nations – South Africa won the first encounter 2-0 on Thursday.
The visitors took the lead through Mukumela in the 36th minute with a long-range shot. Seven minutes later Maluleka opened his account with a thunderous strike that gave the Botswana keeper no chance.
Mbatha increased the lead 10 minutes into the second stanza to make it 2-0 to South Africa.
A minute later Maluleka, who is also the captain, scored his second from the penalty spot after a Botswana defender was adjudged to have handled in the box.
On Monday the South Africans travel to Lesotho for two more matches.
The clashes are part of preparations for the upcoming 2015 African Youth Championship qualifier against Tanzania on Friday, 18 July in Dar es Salaam.
South Africa: Mondli Mpoto, Simon Nqoi, Thendo Mukumela, Keanu Cupido, Khanyisa Mayo (Vuyo Mkatshana), Tshepiso Mahlangu, Charles Baloyi (Vuyo Mantjie), Thato Pheleu (Edwin Sekhwama), Notha Ngcobo, Sibongankonke Mbatha (Thato Ramogogodi), Nelson Maluleka (Felix Noge)