The 26 year old, tied for the lead overnight with compatriots Garth Mulroy and Thomas Aiken, birdied the first and third on the East Course to race two shots clear.
But he found trouble on the fourth, failing to get up-and-down from damp greenside rough and bogeying in wet conditions.
Mulroy and Aiken - both looking for a maiden European Tour title in the event co-sanctioned with the Sunshine Tour - both parred their first four holes to remain one back.
England's Jamie Elson was level par through five to sit 13 under, with another two shots back to Sweden's Oscar Floren.
Aiken drew level at the par three sixth with a magnificent tee shot with five feet, but Schwartzel was back in front when he gained a shot at the par five next.
Schwartzel produced a string of outrageous up-and-downs to remain at 17 under, and when Mulroy and Aiken both bogeyed the 11th, his lead was up to two.
While Schwartzel’s radar from the fairway seemed to have gone awry, there was nothing wrong with his short game and he chipped in from the bunker at the 13th to go to 18 under.
Neither Aiken nor Mulroy converted their birdie putts, leaving Schwartzel three clear with five to play.