South Africa finished superbly after trailing in fifth position with only 500m of the 2km race to go.
Great Britain won silver (6:03.09) and Denmark bronze (6:03.16).
"It was an incredible performance. They kept their cool and came through when it mattered most. We are extremely proud of them and they will be treated as heroes on their return," said Mr Kobus van der Walt, TuksSport Director in his reaction.