Porthen, 21, is a former Junior Springbok captain who has played a handful of games in the United Rugby Championship for the Cape Town-based Stormers, but has impressed coach Rassie Erasmus enough to start.
"Obviously, he has a lot to learn this week, but we have experienced players in the squad who have been helping and guiding him, and we believe this is the right match to give him an opportunity to prove what he can do," Erasmus said in naming his side on Tuesday.
"At this level, you have to sink or swim, so although it will be a challenging week for him to learn our structures, it will also be a very exciting week for him."
Also back in the side are wing Kurt-Lee Arendse, flanker Franco Mostert and lock Lood de Jager, while Sacha Feinberg-Mngomezulu has been selected at fly-half alongside number nine Cobus Reinach.
Centres Damian de Allende and Jesse Kriel will feature with wing Ethan Hooker, which suggests the Springboks will look to play with ball in hand.
Porthen will scrum down in the front row with fellow prop Ox Nche and hooker Malcolm Marx, while RG Snyman partners De Jager at lock and captain Siya Kolisi is in the back row with Mostert and Jasper Wiese.
"Six players in the group are currently plying their trade in Japan, and we believe their experience of playing in that league and either with or against some of their players will be a bonus for us," Erasmus said.
"They (Japan) are a quality team, and they have a top coach in Eddie Jones, so we have no doubt they’ll throw everything at us," added Erasmus.
Japan defeated the Springboks 34-32 in what has become known as the ‘Miracle of Brighton’ at the 2015 Rugby World Cup.
"They beat us in 2015, and they showed what a quality outfit they are in the first half of our 2019 Rugby World Cup quarter-final against them, so we are expecting them to come out guns blazing," Erasmus said.
South Africa team:
15-Cheslin Kolbe, 14-Ethan Hooker, 13-Jesse Kriel, 12-Damian de Allende, 11-Kurt-Lee Arendse, 10-Sacha Feinberg-Mngomezulu, 9-Cobus Reinach, 8-Jasper Wiese, 7-Franco Mostert, 6-Siya Kolisi, 5-Lood de Jager, 4-RG Snyman, 3-Zachary Porthen, 2-Malcolm Marx, 1-Ox Nche
Replacements: 16-Johan Grobbelaar, 17-Gerhard Steenekamp, 18-Wilco Louw, 19-Ruan Nortje, 20-Andre Esterhuizen, 21-Kwagga Smith, 22-Grant Williams, 23-Manie Libbok
