Schwartzel's 12 under par tournament total is one ahead of Zambian Madalitso Muthiya, who followed up his opening round 63 with a 68 on the tougher Firethorn Course.
With a massive 240 player field, the first two rounds are split between Firethorn and the shorter Bushwillow course which Schwartzel tackled in his second round.
Overnight leader Louis Oosthuizen managed nine birdies in his 62 on Thursday, but found the going much tougher on Firethorn with a 70 leaving him on 10 under par, tied for third with last weekend’s Mauritius Open winner, American Kurt Kitayama (69), and home player Zander Lombard (68).
Schwartzel made a steady start with gains on the first and fifth holes, but sprang to life with four birdies and an eagle on his back nine.
The eagle came after a wayward drive on the par five 17th as he chipped in from 75 yards, and could yet be a pivotal moment as he seeks a first win in his home Open championship after twice finishing runner-up.
"It was one of my worst tee shots of the week so far‚" Schwartzel admitted. "I figured if I could walk off with four or five that would be good. I managed to hit a good little third shot there."
Former Masters champion Schwartzel, 34, believes he has been hitting the ball better than ever in practise, but is still looking for his first tour title in almost three years.
"I feel like I've been playing well, I've been hitting very low scores in practise and on the range I'm hitting the ball as good as I ever have. It's just this little thing called golf ... I'm trying to figure it out," he said.
"The golf courses are not playing very long, so if you are hitting it straight you are leaving yourself with a mid-iron into these par fives so you should be taking advantage.
"I would love to win this one, I've given myself a good chance and I'm looking forward to the weekend."
Four-time Major winner Ernie Else (71) is at five under par for the tournament, level on the leaderboard with his nephew, Jovan Rebula (71), who is the leading amateur in the field.
Rebula, 21, claimed the British Amateur Championship at Royal Aberdeen in June.
The highest finishing three non-exempt players this week will gain exemption for the Open Championship at Royal Portrush next July, with 2010 Open winner Oosthuizen already on the entry list.
(Reporting by Nick Said; Editing by David Holmes)
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