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In torrential rain and heavy underfoot conditions, ideally suited to the visitors' powerful forwards, Pat Lambie and Toby Flood traded penalties in the opening half as South Africa took a slim advantage.
A fortuitous try soon after the restart for powerhouse flanker Willem Alberts gave the Springboks the momentum and while England looked threatening at times, South Africa just kept them at bay.
"It could've gone either way.... we were very fortunate... the 50-50s went for us," Springboks coach Heyneke Meyer told reporters.
"I said to Jean (de Villiers) that six months ago this team would have lost this game so after a long season I'll take one point on the day."
England had talked all week about making an impression from the kick off and they rewarded coach Stuart Lancaster immediately, showing much more physical intent than a week ago when they lost to Australia.
A charge down from the first ruck of the game inside South Africa's 22 was followed by a clever and incisive run from winger Mike Brown and the pressure eventually told on the Springboks as Flood landed his second penalty attempt.
While England made most of the early play, South Africa rolled up their sleeves and drew level primarily thanks to lock Eben Etzebeth's spoiling tactics at the line out.
Flood and his South Africa opposite number Lambie were at it again in margins of three before the opening quarter was complete but it was England who looked the more threatening. Two missed penalties from Flood cost them what would have been a deserved halftime advantage.
A desire to front up to the Springboks' monster pack created opportunities for England in the first 40 minutes, none better than to fullback Alex Goode who ran off the shoulder of scrumhalf Ben Youngs, slicing through the ruck and deep inside the visitors' 22.
Whatever South Africa coach Heyneke Meyer said to his players at halftime spurred them into life.
A risky decision to turn down a very kickable penalty a minute after the restart in favour of a lineout proved to be inspired for captain Jean de Villiers.
In propelling himself forward, lock Juandre Kruger left the ball behind and England's attempts to boot it clear failed. Alberts was on hand to scoop up a Tom Wood knock-on from the rebound and score.
A melee inside England's 22 sparked by Etzebeth followed the try but all was forgotten when centre Manu Tuilagi thwarted a threatening South African attack with an intercept.
He charged forward but again England's inability to turn possession and territory into points was telling as Chris Ashton's pass to Brown was a poor one and the opportunity fizzled out.
Lancaster's men attacked with passion and verve in the final quarter and while they closed to within striking distance, debate is sure to rage over England captain Chris Robshaw's decision to kick at goal with less than two minutes remaining and his team trailing by four points.
While the kick was successful, it left England with little time to return to South Africa's half and the Springboks shut down the game to close a long season in the best possible way.
"Credit to South Africa, after a long season... to come here and get the result, credit to Heyneke Meyer and his team," England head coach Stuart Lancaster told reporters.
"But we could've and should've won."
The Springboks now head home after also beating Ireland and Scotland on their northern hemisphere tour while England host world champions New Zealand in seven days' time.