Schwartzel, who started the round a shot behind Englishman Andy Sullivan, carded six birdies in his opening nine holes before finishing with a six under par 66 for a three-round total of 203.
The 30-year-old, who has never won his home championship, is five shots ahead of the Britons, Matthew Fitzpatrick and David Drysdale, who are tied for second.
Schwartzel holed a 50-foot putt on the first to gain momentum. He then holed from six foot and 20 foot for further birdies, before almost pitching in at the fourth.
That created an eight-shot swing over Sullivan who, in contrast to his playing partner's electric start, bogeyed his first four holes.
Sullivan finished with a two-over 74 and trails Schwartzel by seven shots going into Sunday's final round.
Fitzpatrick, a 20-year-old rookie, carded an eagle and six birdies, but also dropped three shots for a five-under par 67. Drysdale sank five birdies in his final seven holes for a 68 having double-bogeyed the 10th.
Another crowd favourite Ernie Els went round in 69, eight shots better than his erratic second round, and is on three under par for the championship in tied 20th.
(Reporting by Nick Said in Cape Town; Editing by Ian Chadband)
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