Kingston finished the final round as darkness set in after an earlier rain delay at the Pearl Valley Golf Estates course. The South African finished at 4-under 284 overall.
'You dream about this, but I never thought it would ever happen,' Kingston said. 'When I saw it was raining I was nervous. The delays just put everything on hold, and it just made the day tougher.'
Wilson started the day with a one-stroke lead, but the Englishman bogeyed three holes on the front nine. He had two birdies on the back to finish with a 73.
Kingston had three birdies on the front nine, but added a bogey and a double-bogey. His birdie on the 11th made the difference.
'I've come close in this championship before and somehow I always thought that this would be it but then I lost,' Kingston said. 'Today was the same situation, but it turned out differently and I'm really grateful.'
Greg Norman shot a 71 and finished in a tie for seventh, and ahead of Ernie Els, Retief Goosen and Angel Cabrera. Els had a 69 to rebound from his second 77 and finish in a tie for 16th with Goosen, who shot a 75.
Darren Clarke (68) tied for third with Kyron Sullivan (71), Louis Oosthuizen (71) and Garth Mulroy (73).
Kingston's victory also secured him the Sunshine Tour's Order of Merit title. Finishing first on the money list earns him a place at next year's British Open and other tournaments.