Tries from Schalk Burger, Breyton Paulse, Andre Snyman and Percy Montgomery sealed the triumph with the Scots stretched for lengthy periods.
Montgomery also struck 16 points with his boot, while a Simon Webster touchdown and three Chris Paterson penalties and a conversion consoled the visitors.
Dan Parks kicked off for the Scots - but that was the last time a Scottish player touched the ball before the Springboks snatched the lead.
The power of the home pack was instantly underlined as they embarked on a 20-metre rolling maul before Burger made a telling break.
Scotland had wandered offside, giving Montgomery the chance to set up a line-out deep in the danger zone.
The Boks kept up the pressure and Donnie Macfadyen halted Jacob van der Westhuizen with a brilliant tackle.
He spoilt the good work, however, by entering the ruck from side-on and Montgomery collected the easy three points.
Scotland responded in stirring fashion with winger Sean Lamont testing the South African markers down the left flank.
They failed to breach the defence, but Paterson slotted the equaliser from a tricky angle after British & Irish Lion Jason White was blocked off the ball.
Burger then burrowed his way towards the target and appeared to place the ball on the turf a few inches short before rolling it along the grass to the line.
That should have meant a penalty for the Scots, but instead video official Simon McDowell signalled for the touchdown.
Montgomery added the goal and, within two minutes, the challenge of Frank Hadden's side was effectively destroyed.
Burger was again in the spotlight with a trademark charge which provided the time and space for winger Paulse to burst through Mike Blair's tackle and over at the corner.
At the other end, a speculative lob by full-back Hugo Southwell sparked panic in the Springboks' defence and, when Victor Matfield scooped up the ball in an offside position, Paterson calmly reduced the leeway by three points.
Montgomery thumped over a penalty for a scrum offence by Bruce Douglas and the Scots suffered a further setback on the stroke of the interval as Sean Lamont hobbled off to be replaced by Simon Webster.
Paterson gave Scotland a glimmer of hope by confidently completing his penalty treble immediately after the restart but any real prospect of a fightback was dashed when Snyman strolled round under the crossbar following a searing break by Jan de Villiers.
Montgomery converted before adding his third penalty after Nathan Hines obstructed the flow of the ball.
The full-back had the home fans on their feet as he jigged his way past three challenges to collect try number four.
Montgomery continued his spree with another penalty, but there was still time for Webster to skate in for Scotland's consolation try, goaled by Paterson to keep his 100 per cent record with the boot.