Smit is one of five changes to the line-up - he is replaced by Bismarck du Plessis - with fly-half Morne Steyn recalled alongside loose-forward Willem Alberts and loose-head prop Gurthro Steenkamp. Patrick Lambie replaces the injured Frans Steyn at full-back.
Coach Peter de Villiers insists fans should not read too much into Smit's demotion, though, claiming it was pre-planned.
"This is our last chance to look at certain combinations before the Rugby World Cup. We've had these changes in mind since we started our planning for the international season, depending on the injury situation," De Villiers told www.sarugby.net.
Victor Matfield will captain the team for a 16th time in his record 107th Test appearance for the Springboks.
South Africa: Pat Lambie; JP Pietersen, Jaque Fourie, Jean de Villiers; Bryan Habana, Morne Steyn, Fourie du Preez; Gurthro Steenkamp, Bismarck du Plessis, Jannie du Plessis, Bakkies Botha, Victor Matfield (captain), Heinrich Brussow, Willem Alberts, Pierre Spies.