Kingston, a 36-year-old from Rustenburg, South Africa, moved out to a two-shot lead with a 36-hole total of 11-under-par 133 at Durban Country Club.
England's Jonathan Lomas and Andrew Butterfield shot 67 and 69, respectively, to share second place at 9-under-par. Martin Maritz posted the day's best round of 64 and joined fellow South African Tim Clark (70) at 8-under.
U.S. Open champion Retief Goosen, the 1995 winner of this event and one of the pre-tournament favorites, headed into the weekend four strokes off the pace after a 2-under 70 that featured a chip-in eagle at the 14th.
Also at 7-under 137 were India's Arjun Atwal (67), Alastair Forsyth (71) of Scotland and South Africa's Ashley Roestoff (71).
Seventeen-year-old South African amateur Charl Schwartzel (67) and 1999 British Open champ Paul Lawrie (70) led a group of seven players at 6-under.
Kingston, a four-time winner on the Asian Tour who also won twice in South Africa last fall, was set to compete in the European Tour Qualifying Tournament but had to sit out after misreading the instructions on the entry form.
'Obviously I am trying to win on the European Tour and it was frustrating that I didn't read the entry form as closely as I should have and missed out on that opportunity,' Kingston said. 'But I feel this is a nice way to get my card rather than going to the Tour School.'
Kingston's best finish in six European Tour starts last year was a tie for 26th at the South African Open, an event co-sanctioned by the European Tour and the Southern Africa Tour.
'I didn't perform as well as I can in European Tour events I entered last season, but I'm hoping to do a little better this time,' he said. 'Who knows, with about 10 events I get into, I could get my card that way. I'm just going to play each shot as well as I can and if I get my card in the end, then so be it.'
Kingston caught fire during the middle of his round Friday, posting six birdies over a 10-hole span from the 5th through the 14th. He three-putted the 16th green for his only bogey, however, then failed to take advantage of the short par-4 18th when he missed a three-foot putt for birdie.
Sweden's Carl Pettersson, the overnight leader after a bogey-free 64 on Thursday, quickly plummeted from the top spot in round two due to a triple-bogey seven at the opening hole. He made five bogeys and just three birdies the rest of the way for a 77 that left him eight shots back.
Ernie Els, victorious at the South African Open in 1992, '96 and '98, had three birdies, two bogeys and an eagle in a 69. He finished tied for 37th at minus-two.
Defending champion Mark McNulty made the cut on the number at even-par 144.
Full-Field Scores from the Bell's South African Open