McGowan shot his nine-under-par round on the par-71 West Course at the Royal Johannesburg and Kensington Golf Club, with four birdies and a bogey on the front nine being followed by an explosive inward nine that featured two eagles and two more birdies.
Behind him is a group of four players on 11 under par comprised of South African duo Jean Hugo and Haydn Porteous, England’s Antony Wall and Felipe Aguilar of Chile.
Wall shot a five-under-par 67 on the tougher East Course while Hugo and Aguilar enjoyed six-under-par rounds of 65 on the West Course, where Porteous went round in 66.
Johan Carlsson of Sweden and Stuart Manley of Wales are a further shot back at 10 under.
McGowan, who finished fifth at the Qualifying School last year to regain his card after injuries stalled his career, impressed with a 67 on the East Course on Thursday and he went out in front on Friday in large part thanks to an eagle at the par-four 12th and another at the long 15th.
“I holed a wedge at 12 today which was nice and then I hit two great shots into the par five, so I had 15-20 feet there for eagle and managed to hole that one as well,” the 33-year-old former Madrid Masters winner told www.europeantour.com.
In a tournament that has seen players play a round each on two different courses over the first two days, there is extra incentive for the field with three places available at this year’s British Open at Troon to players who finish in the top 10 and are not already exempt.
One man who is already exempt is Ernie Els, the two-time former British Open champion, who had a two-under-par round of 70 on the East Course to sit just the right side of the cut at three under.
First-round leader Justin Walters of South Africa is in a tie for eighth on nine under par after following his opening 65 on the East Course with a two-under 69 on the West Course.
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