The Springboks crushed any hope of a first Scottish win in South Africa with a commanding victory in Durban.
Tries from Schalk Burger and Breyton Paulse in the first quarter helped them to an 18-6 interval lead, two penalties from Chris Paterson the only riposte.
The Scotland wing added another on the resumption but further scores from Andre Snyman and Percy Montgomery put the outcome beyond doubt.
Simon Webster scored a consolation try for Scotland with three minutes left.
Paterson added the conversion to put a modicum of respectability on the scoreline, but in reality it was a rude awakening for the Scots after their Six Nations heroics.
Montgomery kicked the hosts into an early lead but Paterson levelled when Boks number eight Joe van Niekerk held back Jason White as the Scots pressed for a try.
Scotland suffered a let-off when South Africa wing Snyman spilled the ball, and the Boks were unfortunate not to score after a 20m driving maul over the Scots' line.
Replays were inconclusive and after referring it to the video referee, Scotland escaped with a 5m scrum.
But South Africa got the benefit of the doubt from the resultant scrum when Burger dived through a mass of bodies, even if it appeared he was held up narrowly short.
TV official Simon McDowell was called into action for a third time two minutes later, and this time there was little doubt about the try.
Paulse took a return pass from scrum-half Fourie du Preez and bounced out of Dan Parks' tackle before holding off Donnie Macfadyen's despairing effort to dot down in the corner.
Scotland struggled to make any real headway
Montgomery missed the conversion and a subsequent penalty, and Paterson rewarded only the second Scottish foray into Springboks territory with another penalty to make it 15-6.
The goal-kicking wing was then forced into a last-ditch tackle on Jaco van der Westhuyzen as they struggled to keep the hosts at bay.
Montgomery rediscovered his aim to extend South Africa's lead with another penalty, but the visitors escaped without further damage as they limped into the interval 18-6 down.
Scotland brought on hooker Dougie Hall and prop Craig Smith at the interval to bolster their front row, and Paterson kicked his third penalty after 44 minutes to keep them in touch.
But South Africa scored their third try after 55 minutes as Jean de Villiers exposed a weakness in the Scots' defensive line.
Parks moved up too quickly and the big centre surged between the fly-half and Marcus Di Rollo before putting the supporting Snyman over for a simple try.
Montgomery's conversion made it 25-9, and he added another penalty on the hour to extend the Boks' lead.
Moments later the full-back cut inside to finish off a flowing move featuring a powerful charge from lock Danie Rossouw.
Montgomery banged over another penalty with 10 minutes left before the Scots roused themselves to fashion a score for Webster, but it was far too little, too late.
South Africa: P Montgomery; B Paulse, J Fourie, J de Villiers, A Snyman; J van der Westhuyzen, F du Preez; O du Randt, J Smit (capt), E Andrews, D Rossouw, V Matfield, S Burger, J Smith, J van Niekerk.
Replacements: W Olivier (for De Villiers, 54), L Sephaka (for Du Randt, 56), P Wannenburg (for Van Niekerk, 60), E Januarie (for Du Preez, 60), G du Toit (for Paulse, 62), Muller (for Matfield, 70), H Shimange (for Smit, 75).
Scotland: H Southwell; C Paterson, M Di Rollo, A Henderson, S Lamont; D Parks, M Blair; G Kerr, S Lawson, B Douglas, N Hines, S Murray, J White (capt), D Macfadyen, A Hogg.
Replacements: S Webster (for Lamont, 39), D Hall (for Lawson, 40), C Smith (for Douglas, 40), A Kellock (for Murray, 59), G Ross (for Parks 63), K Brown (for Hogg, 67), S Pinder (for Blair, 73).
Referee: Donal Courtney (Ireland)