First-round leader Morten Orum Madsen maintained a share of the top spot with a 71 at the Leopard Creek Country Club.
Madsen won for the first time on the European Tour last week and is trying to become a back-to-back champion.
"I've got a bunch of confidence right now," said Madsen. "I really believe that I'm going to hit good shots on pretty much every shot.
Richard Finsh and Tyrone Van Aswegen were tied for fifth at 138, but Finch could have been in much better shape. He played his final four holes in 4-over on the way to a 70.
This is the second straight week Schwartzel and Madsen have gone head-to-head in a battle for the title. Schwartzel held a one-shot lead over Madsen going into the last round of the South African Open Championship a week ago.
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