First-choice number nine Faf de Klerk has been released back to his English Premiership side Sale Sharks by prior arrangement, leaving coach Rassie Erasmus with inexperienced options in that position.
Ivan van Zyl, who started the 12-11 defeat by England in the opening match of the tour, will be on the bench.
The rest of the backline remains the same that played in the dramatic 29-26 win over France last weekend, with Handre Pollard leading the attack from flyhalf and Willie le Roux adding experience at fullback.
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A calf injury to number eight Warren Whiteley, which has seen him released from the tour group, has prompted significant movement in the pack as Duane Vermeulen shifts from flank to take his place at the back of the scrum.
Pieter-Steph du Toit moves from lock into the number seven jersey with RG Snyman coming off the bench to partner Franco Mostert in the second row.
Erasmus had hoped to have Eben Etzebeth back from injury for the Scotland test but was left disappointed.
"Unfortunately Eben is still not fully fit, which gives RG Snyman another great opportunity to start against one of the top rugby sides," Erasmus said in a media release from SA Rugby on Thursday.
"Moving Duane and Pieter-Steph around in the pack isn’t disrupting at all as both of them are very experienced and have played for us in these positions earlier in the season."
The Springboks are looking to become just the second side, after world champions New Zealand, to defeat Scotland in 10 home tests at Murrayfield.
But Gregor Townsend’s team has a strong home record, having beaten Ireland, England, Wales, France and Australia.
"Scotland is a well-coached side, they are difficult to break down and they will present us with a very tough challenge at Murrayfield," Erasmus said.
"The matches in the northern hemisphere are all closely fought encounters, with the set-piece battle key, and it’s important to grab the big moments and finish your opportunities."
Team: 15-Willie le Roux, 14-Sbu Nkosi, 13-Jesse Kriel, 12-Damian de Allende, 11-Aphiwe Dyantyi, 10-Handre Pollard, 9-Embrose Papier, 8-Duane Vermeulen, 7-Pieter-Steph du Toit, 6-Siya Kolisi (captain), 5-Franco Mostert, 4-RG Snyman, 3-Frans Malherbe, 2-Malcolm Marx, 1-Steven Kitshoff
Replacements: 16-Bongi Mbonambi, 17-Thomas du Toit, 18-Vincent Koch, 19-Lood de Jager, 20-Francois Louw, 21-Ivan van Zyl, 22-Elton Jantjies, 23-Cheslin Kolbe.
(Reporting By Nick Said; Editing by Kirsten Donovan and Jon Boyle)
