The 31-year-old averaged a modest 26.14 during the recent 5-0 Ashes triumph over England, reaching 50 just once in eight innings.
However, he displayed explosive form in Perth, where he took James Anderson for a world record-equalling 28 runs in one over.
National selector John Inverarity said: "We believe this is a strong squad with sufficient flexibility for this great challenge of taking on the world's top-ranked Test team. George Bailey, who played an important role in the Test team that defeated England 5-0, has been overlooked for this tour.
"This was a difficult decision, but on this occasion we felt Alex and Shaun have games that are well suited to facing South Africa in South Africa. We consider that both are strong players of pace bowling which is important given the strength of South Africa's attack.
"Alex was on standby for the recent fifth Test in Sydney and scored a most impressive 165 not out against South Africa for Australia A last season. Shaun is a talented batsman who is striking the ball very well at the moment. He has the technique and potential to do well."
Australia squad: Clarke (captain), Haddin (wicketkeeper), Bird, Doolan, Faulkner, Harris, Johnson, Marsh, Lyon, Pattinson, Rogers, Siddle, Smith, Warner, Watson.