Scotland had enough chances to claim their first victory over the Boks in six attempts but a series of missed penalties, including a glaring, late 15-metre miss from Phil Godman, and some determined South African defence, saw the Boks build on last weekend's narrow win over Wales.
South Africa now travel to Twickenham as they complete their autumn series with a match against England, while Scotland know they will be unseeded for the 2011 World Cup in New Zealand. Frank Hadden's men had to beat the Boks to remain in the world's top eight and therefore secure an automatic seeding but defeat means they could be drawn with two of the world's premiers teams for the tournament's group stages in three years time.
The Boks lost hooker Bismarck du Plessis to a leg injury inside the opening five minutes, meaning skipper John Smit was forced to move across the scrum from tighthead prop. Smit played a full 80 minutes at tighthead for the first time in eight years last Saturday but du Plessis' misfortune means Peter de Villiers will be forced to wait to assess the impact Smit can have at the fulcrum of the front row.
Scotland were then forced to make a permanent change of their own as influential full back Chris Patterson came off worse in a collision with Springbok openside Juan Smith. Having calmly collected a high ball, Paterson evaded the onrushing Adrian Jacobs but clattered straight into Smith, injuring his cheekbone and ending his involvement in the afternoon's proceedings.
After a disjointed opening, it was the home side who were gifted the first chance to put points on the board with the game 10 minutes old. Schalk Burger's decision to use only his shoulder and not his arms in a tackle presented Dan Parks, an early blood replacement for Godman, with a straight-forward penalty.
The Glasgow Warriors outside-half failed to add to his 101 international points, however, as he fluffed his kick at goal from just 10 metres to the left of the posts and 25 metres out.
Despite the nature of his first penalty miss, Parks had no hesitation in accepting a second shot at the sticks when the Boks were again penalised on the edge of the 22. His confidence was misjudged as he again made a poor contact to send his effort scurrying wide of the near post from eight metres in from the left touchline.
Scotland could argue to have had the better of the early exchanges but the Boks should themselves have taken the lead with 20 minutes played. Having successfully landed all four of his kicks at goal in the 20-15 win in Cardiff, fly-half Pienaar would have expected to put his side 3-0 in front when handed an opportunity from 15 metres to the left of the posts on the edge of the Scotland 22.
Despite a clean connection, Pienaar's kick failed to find its target, leaving the game still scoreless entering the second quarter.
The deadlock was finally broken by Godman, who had returned to the field to widespread applause to take the place of Parks. Wearing a prominent bandage across his forehead, Godman had little difficulty with his 25-metre penalty effort as Scotland edged 3-0 ahead with 26 minutes on the clock.
Scotland continued to enjoy the lions' share of territory but it was South Africa who came closest to registering the game's first try after 31 minutes. A typically-incisive break from outside centre Jean de Villiers put the Boks on the front foot, with Jacobs quickly transferring the ball to Conrad Jantes. The full back was tackled just outside the opposition 22 but the Boks recycled ball quickly and spread play to the far right-hand side, where JP Pietersen was held up over the line.
Pietersen came off his wing to again threaten from the resulting five-metre scrum but the move came to an abrupt end as referee Dave Pearson penalised former IRB World Player of the Year Burger for diving straight over the top.
Godman missed a drop goal four minutes later but the Scottish supporters didn't have to wait long before their side moved further ahead. It was the impressive half backs who were the catalyst for Scotland's first home try since the World Cup win over Romania 14 months ago as first Blair and then Godman made telling breaks. Captain Blair burst down the left-hand side to take play into the South African 22, before Godman sliced through the middle two phases later only to be hauled down by Pierre Spies three metres short of the line.
The Scots maintained their composure in the face of some hard-hitting defending as Nathan Hines finally burst through from close quarters. The Perpignan lock broke two tackles after picking and driving from the right-hand side of a ruck on the Springbok line. Godman converted to make it 10-0 Scotland with just two minutes of the half left to play.
South Africa began the second period brightly, with de Villiers again showing his class just two minutes after the teams returned. The Western Province star found space out wide before eventually being bought to ground just centimetres away from his second try in successive weekends. De Villiers had the presence of mind to attempt to pass inside to the supporting Smith but the ball fell short of its intended target and the Scots escaped unscathed.
The Boks did claim their first points of the day three minutes later as Pienaar kicked a simple penalty after Scotland were caught offside deep in their own 22.
The Sharks playmaker, starting only his second Test in the No10 shirt, then made it 10-6 with 54 minutes gone through a second successful penalty.
Things got even better for the Boks three minutes later thanks to sublime piece of finishing from Fourie. The Golden Lions centre, who had replaced Bryan Habana on the left wing, did everything required of him after the Boks had created just a hint of an overlap.
Swift ball retention deep in Scotland territory saw de Villiers give Fourie a sight of the line but, with two defenders frantically covering across, the 25-year-old looked unlikely to register his 23rd try in 41 internationals. Fourie wasn't to be denied, however, as he cleverly slid over the top of Hugo Southwell's desperate tackle before ensuring both feet were in the air, and therefore away from the touchline, when grounding the ball in the left-hand corner.
Pearson chose to use the television match official who, after two minutes' worth of deliberation, confirmed that the Boks had moved a point in front at 11-10.
Pienaar's conversion attempt drifted wide of the far upright but South Africa had dealt the Scots a severe blow by taking the lead for the first time with 57 minutes played.
After Godman missed a 40-metre penalty that would have put Scotland back in front on the hour-mark, Pienaar's third successful penalty extended the Springbok advantage to four points with 15 minutes remaining.
It stayed that way until the final whistle, despite Scotland's best effort. They peppered the Boks' line for close to five minutes but they somehow failed to do add their tally. Godman's missed kick was greeted with 37,000 groans but the Scots still had chances to win it in the dying moments. The Springboks held firm, however, as they gave Ian McGeechan a stark reminder of the extent of the team spirit and camaraderie the Lions will be facing in seven months time.