Powerful Boks burst England bubble
England went into the match as slight favourites following wins over Australia and Samoa, but they were no match for the world champions, who bounced back from defeat last week to Scotland with an impressive display of power rugby.
In truth, the Springboks should have won by more and only a late consolation try by Ben Foden added respectability to a scoreline which had never looked in doubt once Lwazi Mvovo and Willem Alberts had touched down for the visitors in the second half.
South Africa enjoyed 70 per cent of possession in the first half and were it not for several butchered try-scoring chances would have gone into the break with a clear lead.
But somehow England found themselves level at 6-6 after Toby Flood and Morne Steyn had swapped penalties, but it was always unlikely they would be able to turn the tide in the second half against a Boks side that dominated the set-pieces and physical battle.
South Africa skipper Victor Matfield was again superb at the lineout and secured more than enough possession for half-backs Ruan Pienaar and Morne Steyn to keep England pegged back in their own half with their accurate kicking.
To be fair to England, they were not helped by injuries to flanker Tom Croft and fly-half Toby Flood, who were both forced from the field in the first half as the home side came off second best in the collisions.
England wing Chris Ashton also took a knock early in the game and never looked in the same fettle as he did in the wins over Australia and Samoa.
Replacements Hendre Fourie and Charlie Hodgson coped well in the circumstances, but by then England were on the back foot to such an extent that one feared that the floodgates would open.
But somehow England kept the Boks out until just before final quarter, thanks in part to an outstanding defensive performance from young lock Courtney Lawes and some poor finishing by South Africa in the first half.
Man-of-the-match Bismarck du Plessis and Mvovo were held up just short of England's try line, and Matfield ignored a two-man overlap and looked certain to score in the 22nd minute before a tackle from Lawes allowed Ben Youngs to dislodge the ball from his grasp.
England scrum-half Youngs had a difficult afternoon, as did most of Johnson's side, and only Lawes and a rejuvenated Mark Cueto can be genuinely happy with their contributions.
Johnson will have tried to add structure to England's game in his half-time talk and issued instructions to cut out the penalties, but within a minute of the restart Steyn kicked the Boks 9-6 ahead after England had again infringed.
The hosts enjoyed their best period of the game soon after with some route one driving into the Springboks defence but were unable to comes away with points after sustained pressure in the Springboks 22.
England's scrum had been under pressure for most of the afternoon and when they lost one against the head just before the hour South Africa were handed another attacking opportunity.
Prop Tendai Mtawira was held up just short but when the ball was recycled Pierre Spies put replacement flanker Alberts over in the corner for his second try of the autumn.
Ten minutes later Morne Steyn dropped back in the pocket after another series of South African drives. But instead of the ball going to the fly-half it was moved to the left wing where Mvovo evaded the tackles of Ashton and replacement Simon Shaw to burst clear for the Boks' second try and a 21-6 lead.
The game lost its shape as both sides made changes late on but to England's credit they continued to attack the Boks at every opportunity.
Mike Tindall came close after he was driven towards the Boks try line and replacement prop David Wilson and Fourie also carried well in the closing stages.
With two minutes to go South Africa looked to have an overlap but replacement prop CJ van der Linde spilled the ball after a splendid tackle by Wilson. Foden scooped up the loose ball and sprinted clear from his own 22 for England's late try.
Tindall made a hash of a quickly-taken conversion but it proved irrelevant to the scoreline.
South Africa were the better side by some margin and Johnson's assertions earlier this week that England are a work in progress proved to be spot on.