The 2011 Masters Tournament champion spoke ahead of the week at Randpark Golf Club of his belief that he was playing the best golf of his career but not getting the rewards to show for it as he seeks a first win since 2016.
An opening 67 on the tougher Firethorn Course on Thursday gave the home favourite an excellent foundation and he built on that brilliantly over the Bushwillow in round two to move to 12 under.
Zambia's Madalitso Muthiya was at 11 under, a shot clear of South Africans Louis Oosthuizen and Zander Lombard, and last week's winner Kurt Kitayama.
Schwartzel has claimed eight of his 11 European Tour wins on home soil but his national Open has so far eluded him, with two runner-up finishes and a further four top fives.
The 34 year old began quietly compiling a handy score, birdieing the first and fifth to turn in 33 and adding further gains on the 11th, 12th and 14th.
A long putt on the 16th had him within one but a poor tee-shot meant he had to lay-up ahead on the 17th. That proved no problem as he hit his third into the back fringe and spun the ball back into the cup for a spectacular eagle and the lead.
“The drive on 17 was probably one of my worst tee-shots for the week,” he said. “I figured if I could walk off with four or five, it would be good. I managed to hit a really good little third shot there. They don’t happen very often.
“I still can’t figure out why I’m not getting the performances I need, even after that round. I’ve had a few tournaments where I’ve played well like this, so I’m not going to talk too much yet.
“There’s lots of golf to play. All I know is I’m playing well. I’m driving the ball well and I haven’t been doing that consistently.”
Muthiya birdied the fourth to join the lead but gave the shot back on the eighth before a gain on the ninth saw him turn in 34 on the Firethorn.
He birdied the 12th before a three-putt double-bogey on the next sent him tumbling back but he responded in brilliant fashion, birdieing the 14th and 15th and making a 12-footer on the 16th to lead alone again as he one-putted his final five holes.
Kitayama quickly picked up where he had left off on Thursday with a birdie on the first but he bogeyed the sixth before recovering on the seventh to turn in 34 on the Bushwillow. The American birdied the par-five 12th and 17th on the back nine but dropped a shot on the 16th.
Lombard produced a brilliant opening 64 on the Firethorn but was in danger of squandering that when he paired three birdies on the front nine with a bogey on the second and a triple on the third to turn in 36.
Birdies on the 11th and 12th moved him back into red numbers and he got on the green in two at the 17th to make an eagle and get into double figures.
Oosthuizen was behind a sapling off the tee on the first for an opening bogey and then made ten pars in a row before finding his gear on the Firethorn. He sandwiched a beautiful approach on the 13th with birdies on the par-five 12th and 14th but dropped a shot on the 16th.
South African Jbe Kruger and Zimbabwean Mark Williams were at nine under, a shot clear of Branden Grace and Matt Wallace, and two ahead of Thomas Aiken and Yikeun Chang.