In second place on 66 in the European Tour event at Glendower Golf Club was fellow South African Shaun Norris, one ahead of compatriots Keith Horne and Jbe Kruger.
A threat of lightning meant play was suspended late in the day with 33 players still out on the course. They will return to complete their rounds on Friday morning.
Van Zyl was among the title contenders in the first two events of the 2015-16 European Tour season at Leopard Creek and Sun City before Christmas and set the pace on Thursday. The 36-year-old carded an eagle and six birdies but dropped a shot at the par-four seventh hole following a poor chip on the edge of the green.
The South African Open is the first tournament of the year in which players are no longer permitted to anchor the club to the body while putting.
Norris had previously used the anchoring method but showed no ill-effects from the change.
"I was tinkering around in the off-season and I eventually found something that feels good. I hit a couple of very good putts today and it seems to be working," he told reporters.
"Changing to the short putter, I didn't really feel like I was that uncomfortable. I just stuck to it and trusted it."
Double U.S. Open champion Retief Goosen returned a 68 while fellow South African and former world number one Ernie Els opened with a 73.
(Reporting by Mark Gleeson; Editing by Tony Jimenez; mark.gleeson@thomsonreuters.com; +27828257807; Reuters Messaging: Reuters Messaging: mark.gleeson.thomsonreuters.com@reuters.net)
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