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Pienaar finished with 20 points while all England could muster were two penalties for fly-half Danny Cipriani, who endured another forgettable afternoon.
The Springboks had stuttered to victories over Wales and Scotland and head coach Peter de Villiers claimed during the week his side were mentally fatigued and struggling for motivation.
It proved to be the smokescreen many expected, as South Africa produced a ruthless attacking performance and monumental defensive display.
Once again, England contributed to their own demise and were booed on the final whistle after an embarrassingly impotent performance.
The 36-point margin smashed England's previous heaviest Twickenham defeat, a 41-20 defeat to the All Blacks in 2006.
When Johnson warned after last Saturday's defeat to Australia there would be "worse days than this", he would not have envisaged only have to wait a week.
He had urged England to "play smart" and they started positively, with Nick Easter winning a penalty for Cipriani to convert.
England won the first-half turnover battle 5-0 but once again they created very little, allowing the Springboks to soak up the pressure and pounce.
After Delon Armitage and Ugo Monye had made little ground, Steve Borthwick tried to create a platform but was penalised for holding on and Pienaar drew the Boks level.
Cipriani missed with a long-range penalty but then put South Africa in deep trouble with a clever chip under the posts after a surging break down the right from Sackey.
Tom Rees chased well to charge down Habana's clearance and earned England a five-metre scrum but the South African defence held firm until the ball was hacked clear.
The Springboks surged down the other end of the field and showed England exactly how it should be done.
Borthwick recovered a messy situation to concede a five-metre scrum as Ricky Januarie threatened to dive on a loose ball - but the Springboks scored straight from the set-piece.
The combined efforts of Cipriani, Riki Flutey and Jamie Noon could not halt flanker Danie Rossouw, who stretched to score under the posts.
Within minutes, England were back under their own posts after Cipriani had a clearance blocked down and Pienaar raced clear to score.
It was the third time in six Tests Cipriani has conceded a try from a charge-down. The same happened against Italy in the Six Nations and the Pacific Islanders a fortnight ago.
England provided one glimpse of attacking ambition when Rees and James Haskell found Armitage out wide but the Springboks closed the gap and John Smit tackled him into touch.
But again England's discipline cost them and they conceded two penalties in quick succession, which allowed South Africa to move within striking distance and Pienaar stretched the Springboks' lead to 20-3.
Cipriani slotted a second penalty as referee Nigel Owens began to lose patience with South Africa at the breakdown.
A minute later the Springboks were reduced to 14 men when prop Tendai Mtawarira was sent to the sin-bin - but England could not take advantage of the extra man.
Instead, Johnson decided to start ringing the changes even before the interval arrived. Flutey had a hamstring problem and was replaced by Toby Flood, while Simon Shaw was sent on for Tom Palmer who did not appear injured.
England began the second half played as if Johnson had put a rocket up them in the interval and piled on the pressure - but once again found the Springbok defence impervious as Bakkies Botha and then Victor Matfield producing try-saving tackles to halt Easter and then Care.
With all the pressure and momentum, England needed to score but they lost control of the ball at the breakdown and South Africa cleared their lines.
And once again they proved ruthless in attack stretching England before Pietersen slipped a magnificent off-load to Jacobs, who held off Sackey to score the Springboks' third try.
Botha halted Care with another try-saving tackle and Cipriani failed to utilise a two man overlap as England once again left the Springboks 22 empty-handed.
Jantjes was sin-binned for body-checking Armitage but it made no odds to the Springboks, who applied the coup de grace with two tries in the last three minutes.
The first came in a passage of play that summed up the game and England's performance as Matt Stevens lost the ball in contact five metres from the Springbok line.
Sackey dawdled allowing Fourie to gather the clearance and the replacement centre wriggled out of Armitage's tackle to score.
Habana rounded off the Springboks' victory in the dying seconds after England had conceded a free-kick deep in their own half.