With Warren Whiteley unavailable due to a knee injury, flanker Kolisi - who has 28 caps for the Springboks – will take on the role against Eddie Jones' men.
Pieter-Steph du Toit has been named as skipper for the preceding Test versus Wales in Washington on Saturday.
South Africa's director of rugby Rassie Erasmus said: "It's a huge honour to captain the Springboks and Siya and Pieter-Steph are two honest, hard-working men who enjoy the respect of their fellow players.
"I believe both of them will do a good job as captains.
