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Smith's inclusion is one of three changes to the starting XV, with a further four changes on the bench, Saru said in a statement on Wednesday.
Prop Gurthro Steenkamp and lock Eben Etzebeth will start in the tight five, with Tendai Mtawarira and Bakkies Botha moving to the bench.
Marcell Coetzee will join them among the replacements after coming in as a late substitute for the injured Willem Alberts last weekend.
The final change to the team, which beat Argentina 13-6 last weekend in Pretoria, was the inclusion of flyer Lwazi Mvovo on the bench.
South Africa team: Willie le Roux, Cornal Hendricks, Damian de Allende, Jean de Villiers (captain), Bryan Habana, Handre Pollard, Ruan Pienaar, Duane Vermeulen, Juan Smith, Francois Louw, Lood de Jager, Eben Etzebeth, Jannie du Plessis, Bismarck du Plessis (vice-captain), Gurthro Steenkamp.
Replacements: Adriaan Strauss, Tendai Mtawarira, Frans Malherbe, Bakkies Botha, Marcell Coetzee, Francois Hougaard, Morne Steyn, Lwazi Mvovo.