Seeking a first tournament win in three years, the Swede posted a third round 69 to maintain his overnight lead.
Stenson followed his opening rounds of 66 and 65 with six more birdies but dropped shots at four, 10 and 16 as he seeks his first win on the European tour in five years and a place in the end-of-season Dubai World Tour Championship.
His playing partner and compatriot Magnus Carlsson picked up three shots in the last four holes and is in a tie for second with home favourite George Coetzee.
Coetzee made nine birdies and an eagle on his way to a course record nine-under par 63.
First-round leader Merrick Bremner and fellow South African Darren Fichardt are tied for fourth at 10-under, a further three shots back.
Former world number one Martin Kaymer is tied for sixth, a further two shots back and eight off Stenson’s clubhouse lead, while former Masters champion Charl Schwartzel slipped out of contention in the co-sanctioned European and Sunshine Tour event following a 74.