Joost van der Westhuizen in action for South Africa in 1995
The former Springbok scrum-half, who was a member of the 1995 World Cup winning team, was admitted to a Johannesburg hospital on Saturday morning.
But his charity the J9 Foundation confirmed Van der Westhuizen's death on Monday.
A statement on Facebook said: "It is with great sadness that we confirm the passing of Joost.
Joost van der Westhuizen in the 1999 Rugby World Cup Semi-Final
"He passed away in his home surrounded by his loved ones.
"He will be sorely missed."
Van der Westhuizen, was diagnosed with the condition in 2011, won 89 caps, scoring 38 tries before retiring in 2003.
Joost van der Westhuizen with England players Richard Wigglesworth, Danny Care and Ben Youngs
South Africa rugby president Mark Alexander paid tribute to Van der Westhuizen, calling him one of the best players to ever play the sport.
"Joost will be remembered as one of the greatest Springboks – not only of his generation, but of all time," he said.
"He also became an inspiration and hero to many fellow sufferers of this terrible disease as well as to those unaffected.
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"We all marvelled at his bravery, his fortitude and his uncomplaining acceptance of this terrible burden."