It took a freak try to beat them in a tense, attritional game but coming on the back of last week’s 20-14 loss to Australia, it leaves England needing to beat world champions New Zealand next Saturday to have any chance of earning a top four seeding at the 2015 World Cup draw on December 3.
Stuart Lancaster’s side showed signs of improvement with their decision-making, and they matched the Springboks physically.
But the fortuitous try scored by Willem Alberts at the start of the second half proved decisive.
After winning a penalty deep in the England 22, the Springboks opted to kick to touch and from the attacking lineout, Ben Youngs’s attempted fly-kick rebounded off JP Pietersen and looped towards the tryline. When Tom Wood failed to gather it, Alberts dropped on the ball.
Patrick Lambie, who had earlier kicked three penalties to give South Africa a 9-6 half-time converted from the touchline.
Owen Farrell kicked three penalties to cut the deficit to four points as England fought gamely to snatch the victory.
But the two penalties that Toby Flood missed from the right-hand side in the first half would prove costly.
Flood did kick the six points England scored in the first half, though, as the hosts dominated the scrum but lost the lineout battle in what was a very cagey encounter.
England have now won just one of their last six games under former Leeds coach Lancaster.