Versfeld carded an eagle and four birdies in a bogey-free round, while Santos finished with an eagle to add to four birdies.
Schwartzel had seven birdies, including five on his first six holes, but the 2011 Masters champion failed to fully capitalize on the fast start by making a bogey and a double-bogey around the turn.
Starting at No. 10, he dropped his first shot on No. 17 and then double-bogeyed the par-4 first.
Schwartzel won here by 12 shots a year ago and has also finished second four times at the Leopard Creek course in northern South Africa.
Daly made his return to golf at the BMW Masters in China last month after surgery to repair a damaged tendon in his elbow. He struggled for consistency Thursday with two bogeys and a birdie going out and two birdies and a bogey coming home.