The experienced loose-forward has been named interim skipper after injuries to Jean de Villiers and Victor Matfield mean they will not face the world champion All Blacks.
It is a remarkable turnaround in fortunes for the 2007 World Cup winner, who was so ill from bacterial meningitis after having a cyst close to his spinal cord removed two years ago that his family were advised to say their goodbyes.
"Schalk has been a magnificent servant of Springbok rugby and he fully deserves this responsibility," Springbok coach Heyneke Meyer said in a statement from SARU on Tuesday.
"The resilience he's shown in coming back from serious injury and illness is the kind of qualities I look for in players as well as teams I coach.
"In my eyes, the captaincy is very important and something I never take lightly or want to cheapen. Schalk's character and the fact that he has been a role model for so many through the years made this an easy decision."
Burger will be the 55th player to captain South Africa in tests. The full team for the All Blacks clash will be announced on Wednesday.
South Africa suffered a last-gasp defeat at the hands of Australia in their Rugby Championship opener on Saturday, losing 24-20.
