Fourie was on as a second-half replacement for Bryan Habana
Scotland came close to beating the world champions but were made to pay for missed penalties in a hard-fought encounter at Murrayfield.
Nathan Hines scored the Scots' first home try in 14 months just before the break, adding to Phil Godman's earlier penalty after two Dan Parks misses.
The Springboks hit back with a sweeping move finished off by Jaque Fourie.
Ruan Pienaar added nine points with the boot, but Scotland spurned a scoring opportunity in the final two minutes.
Camped deep inside South Africa's 22m, the Scots continued to recycle the ball, but the visitors' resolute defence held firm against the onslaught.
Hadden regrets missed opportunity
Godman had just spurned a glorious opportunity to cut the deficit to one point - his second penalty miss of the game - as Scotland pushed for the all-important score.
The defeat means Scotland, ranked ninth, cannot now climb back into the top eight of the International Rugby Board's world rankings before the 2011 World Cup draw is made on 1 December, meaning they will be in a group with two top-eight teams.
But despite the result, Scotland coach Frank Hadden can take heart from the way his side matched the Springboks for long periods.
He was forced to make an early change however when goal-kicker Chris Paterson was taken off with an injury, Hugo Southwell coming on at full-back, while Godman needed treatment for a blood wound.
On came Parks at fly-half, but the replacement scuffed two penalty opportunities within the first 15 minutes as referee Dave Pearson penalised South African indiscipline at the breakdown.
The feisty north-westerly breeze hampered Pienaar's kicking rhythm as the fly-half pushed South Africa's first kick at the posts wide on 19 minutes.
The Springboks back row of Juan Smith, Schalk Burger and Pierre Spies were lacking their usual verve and bite around the breakdown as they made basic errors inside their own half.
Flanker Smith wants winning streak
And Scotland finally converted a penalty into three points on 27 minutes when Godman - bandaged up and back on for Parks - split the posts for the first score of the match.
But as South Africa attempted to pound Scotland's tryline, the hosts broke their Murrayfield try famine courtesy of a brilliant break from scrum-half Mike Blair just before half-time.
The captain weaved his way through a gap before finding half-back partner Godman, who was held up just inches short of the tryline.
But the ball was eventually recycled to Hines and the big second row bundled over right by the posts, handing Godman a simple conversion for a 10-0 interval lead.
South Africa came within a whisker of their first try of the afternoon minutes after the restart when Jean de Villiers handed off Ali Hogg, but the centre was taken into touch by a fine try-saving tackle from Southwell.
Hines scored Scotland's try a minute before the half-time interval
With momentum swinging their way, the visitors earned their first points of the afternoon when Pienaar added two penalties in the 45th and 55th minutes.
And with Scotland retreating deeper into their 22m, the tourists took the lead courtesy of a wonderful sweeping move through the backs as Fourie - on for the indifferent Bryan Habana - beat Southwell to the corner.
Although Pienaar missed the conversion, he nailed another penalty to give South Africa a four-point cushion with 14 minutes remaining.
But the score only strengthened Scotland's resolve as they darted, heaved, and burrowed to within inches of the South Africa line, but referee David Pearson's whistle came to their rescue when he blew up for a penalty with just 90 seconds remaining.
Scotland: Chris Paterson, Thom Evans, Ben Cairns, Nick De Luca, Rory Lamont, Phil Godman, Mike Blair (capt), Allan Jacobsen, Ross Ford, Euan Murray, Nathan Hines, Jim Hamilton, Jason White, John Barclay, All-star Hogg. Replacements: Hugo Southwell for Paterson (11), Dan Parks for Godman (43), Scott Gray for White (58), Alistair Dickinson for Jacobsen (64), Rory Lawson for Evans (73), Matt Mustchin for Hines (74), Dougie Hall for Ford (79).
South Africa: Conrad Jantjes, J P Pietersen, Adi Jacobs, Jean de Villiers, Bryan Habana, Ruan Pienaar, Ricky Januarie; Tendai Mtawarira, Bismarck du Plessis, John Smit (capt), Bakkies Botha, Victor Matfield, Schalk Burger, Juan Smith, Pierre Spies. Replacements: Brian Mujati for Du Plessis (2), Jaque Fourie for Habana, Andres Bekker for Botha (61), Francois Steyn for De Villiers (65), Ryan Kankowski for Burger (74), Gurthro Steenkamp for Mtawarira (75), Danie Rossouw (for Spies, 76).
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.