Katlego Mphela's ghosted past his marker to lash onto Steven Pienaar's through ball inside the box in the 44th minute to beat goalkeeper Richard Kingson with a carpet shot.
Bafana Bafana dominated play in the first half and had goalkeeper Khune rarely tested by the Ghanaians.
Ghana coach fielded all his substitutes in the second half handing debut caps to Cofie Bekoe and Bright Addai.
The Ghana bench took off Anthony Annan, Andre Ayew, Haminu Draman, Asamoah Gyan and Lee Addy for Kumordzi, Bekoe, Yaw Antwi, Osei and Addae. Ghana begins its African Nations Cup qualifying campaign away to Swaziland on the weekend of September 3-5.
Ghana line up: Richard Kingson/Daniel Agyei, Samuel Inkoom, Harrison Afful, Jonathan Mensah, Lee Addy/Bright Addae, Anthony Annan/Bernard Kumordzi, Haminu Draman/Yaw Antwi, Agyemang-Badu, Asamoah Gyan/Ransford Osei, Kwadwo Asamoah, Andre Ayew/Cofie Bekoe
Subs: Daniel Agyei, Bright Addae, Cofie Bekoe, Bernard Kumordzi, Ransford Osei, Yaw Antwi