Kingston was at 2-under 142, ahead of fellow South African Andrew McLardy and Welshman Kyron Sullivan, who each shot 71 on the 7,394-yard Pearl Valley Golf Estates course.
Players faced strong winds for the second straight day and Kingston also had a strained neck.
'The ball was oscillating on the greens, and you spend so much energy trying to stand still that it's tough to make a decent stroke, especially on the putts that require a deft touch,' Kingston said.
Greg Norman moved into contention at 1 over with a second-round 70. Ernie Els fought his way back with a 70 -- after an opening 77 -- for an overall 3 over and five shots off the pace.
Norman, who eagled on the par-5 13th, was surprised by his form
'Two weeks ago I played a father-son tournament on the Champions Tour, and I started practicing two weeks before that,' Norman said. 'Prior to that, if I'd played eight to 10 rounds of golf since March I'd be surprised.'
Els also found some inspiration after starting his round with consecutive bogeys.
'A nightmare start, but I stuck with it and tried to make the best out of the day,' Els said. 'But after that start, I could easily have walked off the course with a bad back.'
The difficulty of putting in the gusting conditions bothered Kingston on the first two holes. He missed a 5-footer for birdie on the first, and then three-putted the second from 18 feet for a bogey.
But he eagled the par-5 third before getting pars all the way to the 13th. Then he birdied 14 and 16.
Dutchman Joost Luiten shot a 5 -under 67 with six birdies for the best round of the day, after an 82 on Thursday.