Having triumphed 28-26 over the Springboks on the Gold Coast last week, Australia came out on top again in Saturday's tussle in Brisbane.
The victory takes Australia to within one point of the second-placed Springboks on 10 points, who are five behind leader and reigning champion New Zealand, which beat Argentina in the later game.
Quade Cooper was the star for Australia last time out, converting eight kicks, though he missed his first two-pointer here after Ikitau had crossed following Faf de Klerk's early booking for knocking the ball from Nic White's hands.
Handre Pollard pulled the Boks to within two points with a long-range penalty, though Australia swiftly struck again, Ikitau once more finding the gap and this time Cooper hit his mark from the conversion.
Pollard hit another two penalties either side of a Cooper three-pointer as, back to their full count, South Africa attempted to turn the screw, yet even with Lachlan Swinton seeing yellow (after initially being given a red card for a high tackle) the visitors could not prise Australia's defence open before the break.
Lukhanyo Am finally managed to do so just after the break to nose South Africa ahead for the first time, but it was a short-lived lead, Cooper winning a penalty and converting it before Koroibete steamed in for his first.
Cooper made no mistake and, five minutes later, Koroibete helped himself to his second to wrap up the result – Jasper Wiese's late yellow adding more frustration for the Springboks.