Stenson finished the third round at 16-under 200, three strokes ahead of fellow Swede Magnus Carlsson and South African George Coetzee.
Coetzee charged into second with a course-record 63, which included an eagle on the par-4 fourth hole and a 30 on the front nine. He made 15 greens in regulation.
Stenson played a less-spectacular and somewhat bumpy round Saturday, carding six birdies to offset a trio of bogeys.
First-round leader Merrick Bremner ended the day in fifth place behind Darren Fichardt, who took over fourth at 10-under with a Saturday round of 68.