Matfield, who has been troubled by a hamstring problem, takes over from John Smit as skipper.
Smit is rested to the bench, with Bismarck du Plessis handed a start instead of Smit at hooker.
"It is the first time since our first game that we have the privilege to select the team from 29 fit players," Springboks coach Peter de Villiers said.
"The one thing that stood out in the Samoa v Fiji game (last Sunday) was how good Samoa were at scrum time.
"They annihilated the Fiji scrums, so that is a bit of bother for us. But having Victor back in the lineout, that can be a great contest now. He understands the systems and he inspires people around him."
Team: P Lambie; J P Pietersen, J Fourie, F Steyn, B Habana; M Steyn, F du Preez; T Mtawarira, B du Plessis, J du Plessis, D Rossouw, V Matfield (capt), H Brussow, S Burger, P Spies.Replacements: J Smit, G Steenkamp, C J van der Linde, W Alberts, F Louw, F Hougaard, J de Villiers.
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