An emotional Stone finished the tournament on 14 under par at the Glendower Golf Club, two shots ahead of compatriot Christiaan Bezuidenhout following a remarkable fourth round that had just five pars.
The 22-year-old Stone carded a 71 containing seven birdies and six bogeys as his fortunes swung wildly under the hot African sun.
Bezuidenhout, 21, carded a 67 for his 12-under-par total. A shot back in third was Englishman Daniel Brooks, who bogeyed the last for a disappointing 72 and an 11-under-par score.
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Stone had established a two-shot lead during the rain-hit third round that had to be finished on Sunday morning.
He then raced into a five-shot lead in what seemed an unstoppable charge for his home championship before bogeying six of the seven holes between the fifth and 11th in his final round.
A birdie on the eighth was his only respite, but after stopping the rot with another birdie on the par-four 12th Stone’s fortunes swung again as he picked up shots on four of the next five holes.
“I don’t have the vocabulary to describe how I feel right now, that round was the most up and down one I have had in my life,” Stone told reporters.
He was in tears on the 18th green and said the round mirrored his recent golfing fortunes.
“Walking up the 18th made me think about the last few years too, which have been so up and down for me.”
An excellent iron into the 12th green sparked the birdie rush that would take him to the title.
“After making the bogey on the 11th, I said to myself, 'come on, you’re still leading the golf tournament, you have been playing great for three days now. Let’s just keep it going'.
“My first target was just to hit the fairway on 12, then to get close to the pin. I hit an incredible shot and it just swung from there. Once I got the birdie back I felt I was ready to get going.”
(Reporting By Nick Said; editing by Clare Fallon)
