Harding, who missed the cut in his previous two European Tour tournaments in 2016, carded a seven under-par 63 and is one shot ahead of compatriot Michael Anthony (64).
Home golfer Thesis Spangenberg, who only came through the qualifying tournament on Tuesday to take his place in the field, continued that form with a five under-par 65, despite a double-bogey on the 10th hole.
South African Open champion Brandon Stone carded a disappointing one over-par 71, but at least took bragging rights in his family after father Kevin was four shots worse off following his opening round.
It is not the first time the Stones have gone head-to-head on the European Tour, they also played in the Joburg Open last season.
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(Reporting by Nick Said; editing by Justin Palmer)
