Kingston was joined in the lead at 11-under-par 132 by Hennie Otto (67) and Jakobus Roos (65).
'I am a little bit surprised to be in this position as I hadn't played a lot of golf coming into the week,' Kingston admitted. 'In fact mentally, I'm probably still in Mozambique on holiday.'
Terry Pilkadaris is alone in fourth at minus-10 with Ariel Canete, Dean Lambert and Louis Oosthuizen one stroke back at 9-under-par 134.
The event used the East and West Courses of the Royal Johannesburg and Kensington Golf Club for the first two days. The East course is a par 71, while the West is a par 72. The 83 who made the cut will play the East Course the final two rounds.
Kingston was steady out of the gate with one birdie over his opening eight holes. He poured in an eagle at the par-5 ninth on the West Course to move to 8 under.
The South African ran off seven consecutive pars from the 10th. Kingston birdied the 17th and then drained an 8-foot eagle putt on the 18th to grab a share of the lead.
'This morning I was getting a little bit frustrated because you saw the scores from Thursday on the West Course and everybody seemed to be shooting the lights out here,' said Kingston. 'So to be 1 under after eight holes was a little frustrating. But then I got the eagle on the ninth and although nothing seemed to happen again for a while on the back nine, to finish the way I did, suddenly it turned into a good round.'
Roos, who started round two tied for 28th, collected back-to-back birdies from the second on the West Course. He tripped to a bogey on four, but atoned for that error with a birdie at the seventh.
He carded five pars in a row around the turn. Roos birdied the par-4 13th and made it two straight as his birdied 14 as well. Like Kingston, Roos played the final three holes in 3 under with a birdie on 17 and an eagle, from 5 feet out, at the last.
Otto traded a birdie for a bogey from the second. He ran off three birdies in a five-hole span from the sixth to climb to minus-9.
The 30-year-old birdied the 15th to move within one of the lead. Otto birdied the par-5 closing hole to gain his share of the lead.
Andrew McLardy, who led after round one, stumbled to a 1-over 72. He shares eighth place at 8-under-par 135 with Magnus A. Carlsson, Alastair Forsyth, Doug McGuigan, Edoardo Molinari, Mark Murless, Henrik Nystrom, Magnus Persson, Richard Sterne, Jaco Van Zyl and Matthew Zions.
The cut line fell at 3-under-par 140 with 83 players advancing to the final two rounds.