The 23-year-old winner of one competition on the circuit carded seven birdies at Leopard Creek Country Club, which borders Kruger Park game reserve in north-eastern South Africa.
His only slip on a hot early southern hemisphere summer day was a bogey four at the 12th hole of a 6,663-metre (7,287-yard) layout carved out of thick bush.
Defending champion Charl Schwartzel, fellow South African Keith Horne and Chris Hanson from England share second place on 202.
Former US Masters champion Schwartzel, seeking a fifth Dunhill victory in 12 attempts, fired a 68, Horne a 67 and Hanson a 68 over the par-72 track.
After reaching the turn in a level-par 35, Schwartzel collected five birdies in six holes to move within two strokes of Stone.
However, he came unstuck at the par-three 16th, finding water from the tee, and holing a difficult putt for a bogey four.
Stone, cautious after seeing what happened to playing partner Schwartzel, found thick green-side rough at the same hole, but saved par with a pitch and challenging putt.
Both golfers parred the last two holes despite a wayward tee shot from Schwartzel at 18 and an equally poor second shot from Stone on the same hole.
Hanson, the lone non-South African among the top four on the leaderboard, carded three birdies and one bogey on his outward nine.
But the Englishman parred only one hole on a rollercoaster inward nine that included five birdies and three bogeys.
Scot David Drysdale fired a 64 -- the lowest round of the week -- to lie six shots behind 2016 South African Open champion Stone.
A flawless round for a golfer seeking his first European Tour victory after 20 years as a professional included five birdies on the first nine and three more on the second nine.
Copyright AFP (Agence France-Presse), 2016