The event is not official on the 2009 European Tour schedule.
Goosen's total, 12-under 204, leads reigning Masters champion Angel Cabrera (68) of Argentina and first-round front-runner Robert Allenby (68) of Australia.
A storm interrupted play for an hour.
Goosen wooed a native crowd with a late rally after Allenby played his first 10 holes in 4-under par.
Defending champion Henrik Stenson (70) of Sweden shares fourth with England's Ross Fisher (66) at 8-under 208.
Ireland's Rory McIlroy, who teamed with Graeme McDowell for a strong start at the World Cup of Golf, was forced to withdraw from the elite 12-player event Saturday due to an undisclosed illness.
Copyright 2009 by United Press International.
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