The pair led the tournament after the third round on 14 under par and went head-to-head after the fourth round was abandoned because of torrential rain which left parts of the course under water.
The 27-year-old Naidoo, ranked 466th in the world, birdied the par four 18th after a pitch to the green put him almost on top of the pin.
"It feels like a dream, it’s overwhelming," said Naidoo, whose Indian heritage made him a popular figure with the crowds in Durban, which has a large Indian community.
"I felt like I was Tiger Woods playing out there yesterday with so many people supporting me."
The second and third rounds were completed on Saturday. The final round began at 6.10 am on Sunday but only Chris Paisley, playing on his own, managed to complete his round before play was suspended three hours later.
It was decided to abandon the round and get the co-leaders play off for the title once the rain cleared on Sunday afternoon.