Veteran lock Johan Ackermann replaces the injured Bakkies Botha, who withdrew from the squad after damaging his ankle in Saturday's 34-12 victory over Wales.
The final change comes on the wing, where Akona Ndungane replaces JP Pietersen in the number 14 jersey.
With Smit absent, Sharks second row Johann Muller will captain the team for the second time.
In total, there are six survivors from the starting line-up that defeated England 15-6 in last month's World Cup final.
The fixture against the Barbarians brings down the curtain on South Africa's season - and marks the end of Jake White's reign as coach.
Team: R Pienaar, A Ndungane, J Fourie, F Steyn, B Habana, A Pretorius, E Januarie, CJ Van der Linde, B Du Plessis, J Du Plessis, J Muller (captain), J Ackermann, S Burger, J Smith, R Kankowski .
Replacements: T Liebenberg, H Van Der Merwe, A Van Den Berg, B Pieterse, W Olivier, W Julies, C Jantjes.