The Golden Lions forward replaces namesake Flip van der Merwe, who is suspended after being found guilty of striking Australia winger Joe Tomane with his forearm in the Springboks' 28-8 victory in Cape Town on Saturday.
The lock swap is the only change to the squad that was named against the Wallabies as coach Heyneke Meyer kept faith with the players that have won four of their five Rugby Championship matches this season.
The 30-year-old Van der Merwe has been named on a number of South Africa squads since his first call-up in June 2012 but has yet to be given a cap.
His familiarity with the Springboks environment appears to have earned him the nod for the tournament decider.
"Losing any player, for whatever reasons, is never ideal but Franco knows our structures and plans very well, having been part of the squad since June last year," Meyer said in a statement on Monday.
Other locks in the squad include uncapped Sharks youngster Pieter-Steph du Toit, Juandré Kruger and regular starter Eben Etzebeth.
Meanwhile, the Springboks are assessing the fitness of inside centre JJ Engelbrecht following the victory over Australia. He is nursing an injured quad muscle and will be given a fitness test later in the week.
South Africa must beat New Zealand by more than seven points and score four tries in the process to claim the title from the All Blacks.
Forwards: Lourens Adriaanse, Willem Alberts, Marcell Coetzee, Bismarck du Plessis, Jannie du Plessis, Pieter-Steph du Toit, Eben Etzebeth, Siya Kolisi, Juandré Kruger, Francois Louw, Tendai Mtawarira, Coenie Oosthuizen, Chiliboy Ralepelle, Gurthro Steenkamp, Adriaan Strauss, Franco van der Merwe, Duane Vermeulen.
Backs: Bjorn Basson, Juan de Jongh, Jean de Villiers (captain), Fourie du Preez, JJ Engelbrecht, Bryan Habana, Zane Kirchner, Patrick Lambie, Willie le Roux, Ruan Pienaar, Jan Serfontein, Morné Steyn, Jano Vermaak.