Coach Rassie Erasmus had confirmed Kolisi in his starting XV on Monday with the proviso that he came through training unscathed to prove his fitness, which the inspirational skipper has done.
"Siya will be starting and he will captain the team," Erasmus said on Tuesday. "It was a hamstring niggle, not something major like he had before 2019 or 2023 World Cups.
"It was a grade-two tear, and it takes a little time to recover, and that's why we've been cautious."
The world champion Springboks are smarting from a 33-16 defeat by the All Blacks at Ellis Park on Saturday after an error-strewn performance and will hope a back-row trio of Kolisi with fellow flanker Pieter-Steph du Toit and No.8 Jasper Wiese will provide the platform for a quick comeback.
The match in Cape Town on Saturday is the second of four Tests and will be followed on consecutive weekends by matches in Johannesburg, scene of the first match, and Baltimore, in the United States.
South Africa team:
15-Damian Willemse, 14-Kurt-Lee Arendse, 13-Jesse Kriel, 12-Damian de Allende, 11-Ethan Hooker, 10-Handre Pollard, 9-Cobus Reinach, 8-Jasper Wiese, 7-Pieter-Steph du Toit, 6-Siya Kolisi (captain), 5-Ruan Nortje, 4-Eben Etzebeth, 3-Wilco Louw, 2-Malcolm Marx, 1-Ox Nche.
Replacements: 16-Deon Fourie, 17-Gerhard Steenekamp, 18-Thomas du Toit, 19-Lood de Jager, 20-Andre Esterhuizen, 21-Cameron Hanekom, 22-Morne van den Berg, 23-Sacha Feinberg-Mngomezulu
