The 2011 Masters champion produced the outstanding golf on a day when the average score was two over par and play was extended into the evening due to a weather delay.
Schwartzel is two shots behind leader and compatriot Anthony Michael, whose score of 69 from a roller-coaster second round left him seven under par for the tournament.
Michael managed four birdies but also dropped three shots as he battled to find consistency on a difficult day on the Pretoria Country Club course.
Tied for third on four under par for the tournament are American Daniel Im (68), and home players Theunis Spangenberg (71) and Haydn Porteous (66), who was a winner at the Joburg Open last month.
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Overnight leader Justin Harding from South Africa had a horror second round which included six bogeys and a double-bogey in a five-over-par 75.
(Reporting by Nick Said; editing by Toby Davis)
