Scotland suffered their fourth straight defeat at Murrayfield, a second-half fightback not sufficient to make up for a first-half bullying by South Africa.
A typically bullish Springboks outfit led 14-3 at half-time, hooker Adriaan Strauss scoring the only try.
Strauss scored again after the break and while replacement scrum-half Henry Pyrgos crossed for the hosts, South Africa's defence kept Scotland at bay.
Defeat means Scotland will finish the year outside the world's top eight.
The consequence will be an unfavourable 2015 World Cup draw when it is made on 3 December, with two other sides from the top eight in the rankings in their pool.
While last weekend Scotland were picked apart by All Blacks guile, this time they were ground into the dust by Springbok brawn before the break.
South Africa were expected to bring intense physicality and directness and they started as expected, Pat Lambie pinning Scotland back with kicks out of hand and forwards and backs running straight and hard, their back row to the fore.
The visitors eschewed an early kick at goal, opting instead to go for the corner, but Lambie did give the Springboks the lead after Scotland were penalised for hands in the ruck.
Greig Laidlaw levelled the scores after South Africa were penalised for not rolling away before Lambie edged his side ahead again after some obstruction.
And Scotland's defence finally crumbled under the heavy shelling when Strauss went over following a kick to the corner and a powerful South African maul.
Scotland lock Richie Gray left the fray after taking a knee to the head, to be replaced by Al Kellock, and there were more groans from the Murrayfield faithful when Laidlaw hooked a penalty wide.
Shorn of Gray's influence, Scotland's defence was splintered again when Francois Louw went on a charge and Lambie popped over the resulting penalty to increase the lead to 11 points.
The hosts finally entered South Africa's 22 after 32 minutes but some sustained pressure came to naught when Kellock was penalised for holding onto the ball.
Having led 14-3 at half-time, South Africa increased that lead to 18 points when Strauss latched onto a long pass from Scotland scrum-half Mike Blair and sauntered under the posts for his second try.
But Pyrgos, only just on for Blair, gave Scotland hope with a training-ground try, the Glasgow Warrior scything through the middle of the line-out after a tap-back by Kelly Brown.
The introduction of Pyrgos seemed to energise the Scottish forwards and there followed a period of furious pressure.
However, a combination of sturdy South African defence and the lack of a cutting edge meant they were unable to convert the pressure into points.
First, Ross Ford's line-out throw on the 5m line was adjudged not to be straightm before a Pyrgos offload to Tim Visser, following a break by Brown, was intercepted.
South Africa's scrum disintegrated in the final 15 minutes but despite earning a string of penalties, and with a man advantage after a yellow card for Springbok replacement Flip van der Merwe, Scotland were unable to breach the vistors' line despite a concerted effort.
Heyneke Meyer's side face England next week looking to complete a clean-sweep of victories over northern hemisphere sides, having also beaten Ireland last week.
Andy Robinson, meanwhile, will be seeking the cold comfort of a victory over Tonga, which would still not be enough to get them into the top eight in the all-important rankings.
Scotland: Hogg; Lamont, De Luca, Scott, Visser; Laidlaw, Blair; Grant, Ford, Murray, Gray, Hamilton, K. Brown, Barclay, Denton.
Replacements: Jackson for Laidlaw (68), Pyrgos for Blair (47), Hall for Ford (68), Cross for Murray (68), Kellock for Gray (22).
Not Used: Traynor, McInally, Murchie.
South Africa: Kirchner; Pietersen, de Jongh, de Villiers, Hougaard; Lambie, Pienaar; Steenkamp, Strauss, J du Plessis, Etzebeth, J Kruger, Louw, Alberts, Vermeulen.
Replacements: M Steyn for Lambie (74), H van der Merwe for Steenkamp (61), Brits for Strauss (76), van der Linde for J du Plessis (52), F van der Merwe for J Kruger (68), Coetzee for Alberts (53).
Not Used: Taute, Mvovo.
Sin Bin: F van der Merwe (76).
Ref: George Clancy (IRFU).