England slipped to a second chastening narrow defeat of the autumn as a disciplined South Africa held them at bay in a frantic, contentious finale.
Two penalties apiece from Toby Flood and his replacement Owen Farrell brought England to within four points after Pat Lambie's boot and Willem Alberts' fortuitous try had opened up a 10-point Springbok lead.
But England's efforts ended in controversy when they opted to kick a late penalty rather than go for the try that would have put them in front.
While Farrell landed the three points there was insufficient time to mount another attack, and a more battle-hardened, streetwise Springbok unit had the win.
It means England have now failed to beat the Springboks in their last 11 meetings, and effectively ends their hopes of a top four seeding going into the draw for the next World Cup.
No team outside of a top four ranking has ever won the World Cup and England will be drawn with one of the top four teams in the group stages of the tournament they will host in 2015.
Wholehearted and hard-working, Stuart Lancaster's men nonetheless lacked both composure and a cutting edge.
And with the New Zealand All Blacks to come at Twickenham next Saturday, there is a strong possibility that they will end their autumn campaign with just a solitary victory over Fiji to show for their efforts.
England had come out of the traps at pace, Geoff Parling charging down Ruan Pienaar's clearing kick from the very first ruck to set up a penalty chance that Flood pulled across the posts from wide right.
Moments later a simpler chance following a side-stepping run from Mike Brown and dynamic series of drives from the forwards allowed Flood put the home side 3-0 up, only for Lambie to level things up from South Africa's first spell in England's 22.
Flood was mangled by three defenders as he attempted to run possession from deep and was helped off the pitch, returning to bang over a second, straightforward penalty before Lambie returned the compliment after skipper Chris Robshaw was penalised at the turning scrum.
England were dominating at the scrum, Flood missing a simple penalty when the Springbok pack was split asunder.
But South Africa were making their few chances count. Lambie made it 6-9 after referee Nigel Owens spotted hands in the ruck, and Tom Youngs was penalised for a crooked line-out to cost his side further momentum.
Better was to come. A slicing break from Alex Goode after a frantic spell on halfway brought the crowd to full voice; Flood tried a grubber into space for Manu Tuilagi to run on to but over-cooked it.
Turnover deep in home territory opened a possible overlap that Ben Youngs - perhaps conscious of his over-adventure last week - chose to kick deep instead, and full-back Zane Kirchner did well to cover and kick clear.
If South Africa were a touch fortunate to lead at the break, there was a significant slice of luck about the try that followed soon after the interval.
A rebound from an attempted kick through gave them territory, and when Juandre Kruger dropped the ball five yards out Youngs' hack clear hit JP Pietersen, eluded Ben Morgan and fell into the grateful grasp of a surprised Alberts a yard out as he flopped over the line.
Lambie added the conversion for 6-16, and as the rain fell the outlook darkened for the men in white.
Only when Manu Tuilagi burst away on an intercept from his own 22 did the atmosphere lift. The centre found Chris Ashton on his inside as he ran out of gas, but the winger's pass to Brown outside him was poor and the opening was gone.
England's struggles at the line-out were intensifying. A fourth loss off their own throw brought a grimace from hooker Youngs, and there was a lack of precision when the ball was put through hands.
Farrell brought it back to 9-16 with 18 minutes left on the clock after Springbok hands in the ruck, but there was a distinct absence of composure and the kicking from hand was poor.
Prolonged pressure and territory failed to yield points. Farrell was struggling to fire the attack; the difficult conditions led to handling errors, and stout defence - with Eben Etzebeth outstanding - snuffed out the rest.
Replacement prop Mako Vunipola spilt the ball when looking to rumble, yet a Springbok error on their own scrum and forwards going off their feet at subsequent ruck gave Farrell an easy penalty for 12-16.
At last the capacity 81,000 crowd began to believe. A scrum penalty on halfway was kicked to touch to set up an attacking line-out on the Springbok 22, and the forwards took it up until replacement hooker David Paice knocked on to howls of dismay.
The seconds ticked away, England battering against a green wall and making minimal inroads.
With two minutes left, a lifeline. South Africa were penalised again, but rather than kicking to touch, Farrell was instructed by Robshaw to take the three points that made it 15-16.
It was a calculated gamble greeted with boos from many in the crowd and when the Springboks took control from the restart it was one that failed.
A game that was winnable had slipped away, and England's weary players sank to their knees as the final whistle sounded.
England: Goode, Ashton, Tuilagi, Barritt, Brown, Flood, B. Youngs, Corbisiero, T. Youngs, Cole, Launchbury, Parling, Wood, Robshaw, Morgan.
Replacements: Farrell for Flood (45), Care for B. Youngs (67), Vunipola for Corbisiero (53), Paice for T. Youngs (67), Wilson for Cole (75), Botha for Launchbury (72), Haskell for Wood (53).
Not Used: Joseph.
South Africa: Kirchner, Pietersen, de Jongh, de Villiers, Hougaard, Lambie, Pienaar, Steenkamp, Strauss, J. du Plessis, Etzebeth, J. Kruger, Louw, Alberts, Vermeulen.
Replacements: H. van der Merwe for Steenkamp (62), Brits for Strauss (74), Cilliers for J. du Plessis (40), F. van der Merwe for Etzebeth (69), Coetzee for Alberts (56).
Not Used: Jantjies, Taute, Mvovo.
Ref: N Owens (WRFU).
Referee: Nigel Owens (Wales)
Assistant referees: Glen Jackson (New Zealand) & Peter Fitzgibbon (Ireland)
TV: Jim Yuille (Scotland)