The swimmer was one of the new board members put in place by South Africa sports minister Fikile Mbalula on Tuesday.
Du Toit, who lost her leg in a motorcycle accident, has been active recently in her support of anti-doping campaigns in South Africa.
Institute chief executive Khalid Galant said Du Toit was "a great role model" for anti-doping. She was the first amputee to qualify to compete with able-bodied athletes at the Olympics.
South Africa will host the World Anti-Doping Conference in November, when a new international anti-doping code will be adopted by sports bodies and could include harsher punishments for offenders.