He becomes the first black leader in a full test match of the national rugby side criticised for failing to redress the racial imbalances of apartheid.
The Stormers flanker was named to lead the Boks against England in June, with previous skippers, loose-forward Warren Whiteley and lock Eben Etzebeth, both ruled out through injury.
The only other black player to lead South Africa was hooker Chiliboy Ralepelle, who was just 20 at the time, in a Springbok XV against a World XV in 2006.
Overlooked last year when then-coach Allister Coetzee preferred Etzebeth despite Kolisi being the lock's captain at the Stormers, the move has significance beyond the field as South African rugby seeks to attract more black players.
Current Bok coach Rassie Erasmus says the decision was based purely on his history with Kolisi but is also aware that it will be a popular appointment with a majority of the South African population.
"I got Siya from the Eastern Cape to come play in the Western Cape. I've known him for a long time," Erasmus said. "I don't want to look at this from a political or historical perspective.
"I coached Siya in his first training session at [Western] Province. I know him as a great rugby player. I've seen him go through good times and tough times as captain and a player. He's a reliable player that always gives his best.
"It's only for the June tests for now as guys like Warren Whiteley and Eben Etzebeth still have to return. It was just common sense that he'd make a good option.
"In terms of what he does for our country is really just a bonus. I like him. He's humble, quiet and gets the job done."
RACIAL TENSIONS
Kolisi's promotion will do no harm as rugby continues to break the shackles of its past image in a country where racial tensions in sport often spillover into politics.
Gwede Mantashe, chairman of the ruling African National Congress and a keen rugby supporter, called Kolisi's appointment an "historic moment" but said more had to be done to increase the numbers of top-level black players.
"He is a good captain. He is a good person. It is quite encouraging. We must see more transformation," Mantashe, who played rugby as a young man in his native Eastern Cape province, told Reuters.
More black players are now commonplace in top-level teams and while Kolisi's selection is a landmark, it is also a natural progression of transformation efforts in the sport, where up until 1981 black players were barred from representing the Boks.
The 26-year-old will not be considered for Saturday's international against Wales in Washington, however, with his Super Rugby franchise team mate Pieter-Steph du Toit wearing the armband for that fixture.
Erasmus announced an extended squad of 43 players for the June tests on Saturday and suggested he would take a number of fringe players to face Wales.
The Boks then host England at Ellis Park in Johannesburg on June 9, before matches in Bloemfontein and Cape Town on the following Saturdays.