Sterne began the final round level with fellow South African Trevor Fisher Jnr on 19-under-par and the battle was tight to begin with, Fisher eagling the first hole while Sterne picked up a birdie.
Sterne birdied the par-three second hole as well after a superb tee-shot to three feet and claimed a one-shot lead when Fisher bogeyed the third.
But the stretch of holes between the sixth and eighth holes was where Sterne really won the tournament and where it all went wrong for Fisher.
Sterne’s precision golf earned him a run of three successive birdies, while a bad miss for par on the sixth and a wayward drive under a tree on the seventh led to consecutive bogeys for Fisher and the 33-year-old was suddenly facing a six-shot deficit as they reached the ninth hole.
Sterne, the 2008 champion, played top-class golf as he closed with a 64, hitting 12 out of 14 fairways off the tee and 17 greens in regulation during his magnificent round.
Despite picking up a birdie on the ninth, Fisher was still in need of a miracle to catch Sterne, but the gap only grew wider as he double-bogeyed the par-four 11th after an awful drive way right into the trees and then a second shot into the stream in front of the green.
Sterne, meanwhile, continued to have the measure of the tough Royal Joburg East Course as he picked up three more birdies on the back nine and finished the tournament with just one bogey in 72 holes.
While Fisher failed to give Sterne any sort of workout on the final day, shooting a 73 to finish in a tie for sixth on 18-under, there was an intriguing battle for second place.
Charl Schwartzel, who has always done well at Royal Joburg, winning the title in 2010 and 2011, eventually muscled his way into the runners-up spot on 20-under with birdies on the last two holes.
Schwartzel was once again in solid form, shooting a six-under 66, but his game just lacked that extra oomph required for him to challenge Sterne.
It was a tough battle though with fellow South African George Coetzee, who shot a 67, and Chile’s Felipe Aguilar and Portugal’s Ricardo Santos, who fired a brilliant 64, finishing on 19-under.
South Africans Keith Horne and Thomas Aiken finished in the tie for sixth with Fisher on 18-under-par.
The 17th hole dished out more misery for Fisher as he three-putted from eight feet and the 2012 Sunshine Tour Players’ Player of the Year was a relieved man when he eventually left the course with a birdie on 18.
Sterne also made birdie on the par-five last hole after blasting out of a greenside bunker to three feet, cleaning up the rest of the field by a record seven strokes.
Schwartzel held the previous records for both the lowest winning score (-23) and biggest winning margin (six strokes), set during his 2010 triumph.
Sterne’s 260 72-hole total has only been bettered five times in European Tour history, by Ian Woosnam, David Llewellyn (both 258), Tiger Woods and South Africans Ernie Els and Mark McNulty (all 259).
Els’s 29-under to win the Johnnie Walker Classic in Australia in 2003 remains the lowest winning score in terms of par, with Sterne now joint second with Jerry Anderson and Louis Oosthuizen.
Oosthuizen’s 27-under 265 to win the Africa Open in East London last year was the previous lowest winning total in a co-sanctioned event in South Africa.