Smit, who led his side to their second Rugby World Cup triumph in France in 2007, returns to the Springbok team as one of five changes from the starting line-up in their last outing against Australia on 30 August.
Brian Mujati drops to the bench to accommodate Smit on the tight head side of the front row and Bakkies Botha takes over from Andries Bekker in the second row after recovering from knee cruciate ligament damage 12 weeks ago.
The return of the 52-times capped Botha means he can extend his second row pairing record with Victor Matfield to 43 games.
Behind the scrum utility back Ruan Pienaar will fill the No 10 jersey in place of Butch James, while pacy wing duo Bryan Habana and JP Pietersen take over from Jongi Nokwe and Odwa Ndungane.
While Springbok coach Peter de Villiers has made changes to his last team, there are still 16 of the 22 that faced and disposed of Wales in the second Test in the summer. The Boks won the Prince William Cup series 2-0 with successive victories in Bloemfontein (43-17) and Pretoria (37-21).
"It wasn't a difficult selection for me to make. The players have shown they are ready to do justice to their selections," said de Villiers.
"We have picked Bakkies Botha from the start because we felt we would run a big risk if we used him as a replacement and he then broke down. We feel it is better for him to play from the start."
"It is going to be a big challenge moving to tight head prop again, but it is one I'm looking forward to. I know that Gethin Jenkins is a formidable opponent," said Smit.
"I haven't played their regularly for a number of years now, although I had a few matches at No 3 for Clermont Auvergne in France."
South Africa: Conrad Jantjes; JP Pietersen, Adi Jacobs, Jean de Villiers, Bryan Habana; Ruan Pienaar, Fourie du Preez; Beast Mtawarira, Bismarck du Plessis, John Smit (captain), Bakkies Botha, Victor Matfield, Schalk Burger, Juan Smith, Pierre Spies.
Replacements: Brian Mujati, Guthro Steenkamp, Andries Bekker, Ryan Kankowski, Ricky Januarie, Frans Steyn, Jaque Fourie.