Scotland produced a much-improved performance to push South Africa hard in Port Elizabeth, but the Springboks did just enough to deserve victory.
Percy Montgomery's goalkicking did the early damage for South Africa, but Simon Webster's well-taken try saw Scotland cut the half-time gap to 12-5.
Chris Paterson had an effort disallowed and South Africa's Fourie du Preez scored to rub salt in Scottish wounds.
A Donnie Macfadyen try cut the gap, but a workmanlike South Africa held firm.
South Africa forced two early penalties, as Scotland's overly eager defence was caught offside, and Montgomery made no mistake with either to enable his side to take a 6-0 lead.
Scotland settled for a limited gameplan early on, content to kick away possession as they looked to build a territorial platform.
The tourists gradually made inroads and the approach paid dividends when, after a long spell of pressure, Webster latched onto Gordon Ross' grubber behind the defence to score out wide.
Montgomery replied with his third penalty to keep his side ahead on the scoreboard, but Scotland's stiff resistance was forcing the Springboks to rely on the boot.
Jaco van der Westhuizen extended his side's lead with a monster penalty from inside his own half but try-scoring opportunities were hard to come by.
In the dying seconds, Scottish livewire Webster made an excellent break before chipping the full-back but the effort was disallowed by the video official for a knock-on in the act of scoring, allowing South Africa to take a seven-point lead into the break.
Soon after half-time, another Montgomery three-pointer - after Jason White was penalised for holding on - put South Africa 15-5 up.
Scotland did not buckle, and when Paterson punished Schalk Burger's offence on the floor with a penalty of his own the boos started to ring out at the EPRU Stadium.
South Africa finally got over Scotland's try-line though, benefiting from a debatable decision from referee Tony Spreadbury.
Paterson intercepted on halfway and raced through to score - only to see his effort disallowed for a knock-on under Scotland's posts several phases before.
From the resulting scrum, South Africa crossed through scrum-half Du Preez to effectively end Scottish hopes.
There was still time for an opportunistic score from Macfadyen after Van der Westhuizen knocked on in his own in-goal area.
But two late Montgomery penalties - when the crowd would have preferred to see a misfiring South Africa run the ball - gave the score a lop-sided look.