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Chris Paterson kicked the home side into an early lead but the Springboks replied with three first-half tries from Bryan Habana, Jaque Fourie and Fourie du Preez to effectively end the game as a contest.
Frank Hadden's side desperately tried to find a way back into the match but struggled to make any holes in the Springboks' watertight defence.
Only the talented Rory Lamont offered a genuine threat to the visitors while the forwards - impressive in recent games - were brought down to earth by thesouthern hemisphere giants.
In contrast, England's World Cup pool opponents, despite missing captain John Smit who has a hamstring injury, demonstrated why they are second favourites for next month's tournament.
Their gameplan was limited, relying on their famously powerful pack, but they also displayed a clinical efficiency when presented with an opening. The terrific Habana was a threat every time he touched the ball.
Yet it was the home side - with Dave Callam and Kelly Brown drafted into the back row - who got into their stride quickest.
Scotland's beefed-up forwards took the game to their much-vaunted counterparts, recycling possession efficiently and making encouraging yards down the middle.
In addition, the enterprising play from full-back of Lamont - who collectedtwo of his own up and unders - helped Hadden's side maintain the early pressure on the visitors.
Scotland were rewarded for their enthusiastic start when Paterson kicked them in front with a straightforward 10th-minute penalty, awarded when the Springboks were penalised for killing the ball in a ruck.
It did not take Jake White's side long to level the scores, though, as Percy Montgomery slotted over an equally-simple penalty three minutes later.
White's men then took the lead in the 22nd-minute when Habana was fed off the back of a scrum by Danie Roussouw and the Bulls winger scorched through a gaping hole in the Scottish defence to score his 22nd try in 28 Tests.
Montgomery added the conversion to make it 10-3 to the visitors and that could have been stretched to 10 points had the recalled Francois Steyn's thunderous penalty attempt from inside his own half been more accurate.
The lead was increased soon after when Fourie touched down in the 25th minute following a line break by Steyn, fit again after a back injury. Montgomery converted to make it 17-3.
The Springboks were now rampant, claiming their third try three minutes later when scrum-half Du Preez fed Montgomery for a charge at the line and, when the full-back was stopped short, picking up and driving over from five yards out.
That ended the scoring for the first half although prop Gavin Kerr, handed a chance to impress in the front row, was replaced by Edinburgh's Allan Jacobsen.
Scotland tried to start the second half as they did the first period but despite plenty of effort could make no headway against the Springboks' aggressive defence.
Hadden sought to freshen his side up just six minutes into the new half when he sent on Scott Murray and Hugo Southwell for Jim Hamilton and Andy Henderson, who had found South Africa's defence considerably more difficult to breach than that of Ireland's a fortnight previous.
Moments later, Lamont further enhanced his claims to the full-back shirt for the World Cup when he hauled down Habana, one of the world's deadliest finishers, a couple of yards short of the tryline.
The visitors showed they were still in a businesslike mode when they chose to kick a penalty 11 minutes into the half through Montgomery's boot rather than opt to attempt to fashion a fourth try.
Hadden made another switch, sending Dan Parks on to play stand-off in place of Paterson, as the home side looked for a way back into the game at 27-3 down.
A plethora of substitutions by South Africa predictably affected the flow of the game with a charge down the touchline by Ally Hogg, on for Callam, being a rare moment of quality rugby.
The greater ball-handling skills of Hogg certainly added a new dimension to Scotland's play in the last quarter and it is almost certain that he will start the World Cup in the back row alongside White and Simon Taylor, who was ruled out of the match against the Springboks with a facial injury.
The margin of victory and the ease with which the visitors blunted the Scotland attack were in stark contrast to the success and level of performance against Ireland a fortnight ago and give Hadden plenty to ponder ahead of the World Cup.
Scotland (3) 3
Pen: Paterson
South Africa (24) 27
Tries: Habana, Fourie, Du Preez
Con: Montgomery (3)
Pen: Montgomery (2)
Scotland: Rory Lamont; Nikki Walker, Rob Dewey, Andy Henderson, Simon Webster; Chris Paterson, Mike Blair; Gavin Kerr, Ross Ford, Euan Murray, Nathan Hines, Jim Hamilton, Jason White, Kelly Brown, David Callam
Replacements: Fergus Thomson, Allan Jacobsen, Scott Murray, Ally Hogg, Rory Lawson, Dan Parks, Hugo Southwell
South Africa: Percy Montgomery; JP Pietersen, Jaque Fourie, Francois Steyn, Bryan Habana; Butch James, Fourie du Preez; Os du Randt, Gary Botha, CJ van der Linde, Bakkies Botha, Victor Matfield, Schalk Burger, Juan Smith, Danie Rossouw
Replacements: Bismarck du Plessis, BJ Botha, Albert van den Berg, Wikus van Heerden, Ruan Pienaar, Andre Pretorius, Ashwin Willemse





