Schwartzel nearly withdrew before play started Friday, but went on to shoot the days second-lowest score to join Fraser (66) at 9-under 133 after the second round.
Englands Robert Rock (65) and Swedens Steven Jeppesen (67) were two shots back. Andrew Tampion of Australia had a 63 that left him five strokes off the pace.
I phoned my dad this morning and he told me to tee off and see how it goes, Schwartzel said. So I did that and then I got a couple of birdies and I started to feel better.
He had a bogey-free round with five birdies and an eagle at the par-5 No. 4.
Im on antibiotics and I dont feel that strong, he said. But that was a very solid round of golf and Im in a very good position.
Fraser, who shot a 67 on Thursday to share the overnight lead, started with three birdies over the first four holes but then made three straight bogeys from No. 6. The Australian rallied with five birdies over the back nine for his 66.
(The course is playing) a bit shorter than other weeks, not so much of a slog-fest, which suits me well because it tests your short game, Fraser said. I feel like Im playing quite well overall.
A handful of players were three strokes behind the leaders, while Spanish Ryder Cup player Miguel Angel Jimenez'who hasnt won in Spain in 10 years' was seven shots back, along with former U.S. Open champion Angel Cabrera.
Jose Maria Olazabals return from an injury lost some momentum after the two-time Masters champion shot a 72 to make the cut at 142.