Andrew McLardy, who held a share of the overnight lead, carded a 1-under 69 and stands alone in second place at 8-under-par 132. Scott Dunlap, the other overnight co-leader, stumbled to a 1-over 71. He is tied for third place with Titch Moore, Sven Struver and Warrick Druian at 6-under-par 134.
Botes opened his round on No. 10 at Wild Coast Sun Country Club and converted birdie attempts at the 14th and 16th to get to 6 under.
Around the turn, he birdied the third before closing his round with back-to-back birdies from the eighth to cap a bogey-free round.
'I know how to win,' said Botes. 'I have just needed to get myself into a position to win again because I haven't been there for a while, so it's good to be in with a chance. I hope it stays calm like it has been over the past two days. I don't mind if the wind blows but I would prefer it if it stayed like this.'
McLardy also began his day on the back side and quickly birdied his first hole. He settled in to run off 10 straight pars before a birdie at No. 3. He stumbled to a bogey at the par-3 sixth for the second straight round.
Bruce McDonald fired a 4-under 66, while Adilson da Silva posted a 3-under 67 to move into a share for seventh place at 5-under-par 135. That duo was joined by Louis Oosthuizen, Gerlou Roux and Andre Cruse, who each posted rounds of even-par 70.
James Holmes carded a 5-under 65 to move to minus-4, where he was joined by Keith Horne, Lewis Atkinson, Ulrich van den Berg, Marc Cayeux, Dion Fourie, Roger Wessels and Michael Archer.
The cut line fell at even-par 140 with 72 players advancing to the weekend.