The famed Scottish running game had the door slammed in its face, while the Boks scored two tries in a five-minute spell at the start of the second half to take complete control of the game.
They had had much of that through a tense first half but were unable to convert it into a return on the scoreboard in front 63 556 fans on a sweltering evening in Marseille.
The Boks mixed characteristic resilience in defence with plenty of ambition in attack and would have been disappointed not to have won by an even larger margin.
But tries by Pieter-Steph du Toit and the prolific Kurt-Lee Arendse in the first 10 minutes of the second half got the job done.
Scotland were under pressure throughout the first half but were hanging on at the break thanks to a penalty goal on the stroke of halftime by flyhalf Finn Russell. He nailed a 45m shot from straight in front after the Springbok scrum was penalised for a second time in quick succession for collapsing.
It was reward for Scottish tenacity as they had hung on throughout a first 40 minutes spent largely between the two 22s, but mostly in the Scotland half. They prevented the Boks from landing a significant blow with the champions having to settle for two penalty goals from three attempts by Manie Libbok.
The Bok flyhalf opened the scoring with his second attempt in the 12th minute – after Russell was penalised for a deliberate knock-on straight in front and 35m out. The second took another 12 minutes to arrive as the Boks struggled to convert a physical dominance into points. Hooker Malcolm Marx was over the ball to win a penalty for not releasing and Libbok slotted from the 22 and 15m in from the left-hand touchline.
Scoring chances were few and far between. Scotland’s sole threat was a right-to-left move with wing Darcy Graham popping up on the opposite flank only to be hunted down by Libbok as he entered the SA 22.
The Boks fluffed their lines from attacks in the red zone with a driven maul being turned over and centre Damian de Allende knocking on after a tap down from another lineout in the 22.
But generally, defences were on top as the importance and the tension of the occasion in a pivotal match in the “Pool of Death” but both teams on high alert to threats.
The scrum penalty trend was reversed in the first minute of the second half, but Libbok’s ambitious 55m attempt fell short. However, the Scottish dam wall was about to burst.
South Africa had an attacking scrum on the right-hand side, five metres out and after De Allende and the thundering Jasper Wiese had been held up, tireless flanker Du Toit came looping round to drive through and the over the Scottish defence.
Four minutes later the Boks had a second try and Arendse his 12th in 11 Tests after a turnover had been won on halfway and after one phase Libbok put in a pinpoint kick pass for the speedster to race on to.
Scrumhalf Faf de Klerk took over the kicking duties (after Libbok’s return was loitering at two successes from five attempts) and duly landed a touchline conversion but then pushed wide a penalty attempt from a similar position.
However, the Boks had opened up a 15-point lead and with a new front on to exert extreme discomfort on the ailing Scottish pack it looked a very long way back for Scotland.
Springboks 18 (6) – Tries: Pieter-Steph du Toit, Kurt-Lee Arendse. Conversion: Faf de Klerk. Penalty goals: Manie Libbok (2).
Scotland 3 (3) – Penalty goal: Finn Russell.