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The Harlequins fly-half - free to run England’s attack with captain Owen Farrell sidelined due to injury - slotted over a last-gasp penalty to seal a dramatic 27-26 victory after an absorbing finish that saw momentum swing back and forth in enthralling fashion in front of a capacity crowd in south-west London.
Saturday’s result means England - who open the 2022 Six Nations against Scotland at Murrayfield on February 5 - finish this year’s Autumn Nations Series with a 100 per cent record after wins over Tonga and Australia, while no1-ranked South Africa’s impressive run is over after they had beaten the All Blacks, Wales and Scotland over recent weeks.
England simply dominated proceedings early on, passing some initial aerial tests and forcing Willie Le Roux to touch down behind his own line before their inexperienced front row with Bevan Rodd and Jamie Blamire - who have only seven caps between them but started due to the absences of Ellis Genge and Jamie George - came out on top at the first scrum.
They kept the pressure on as Smith kicked a penalty to touch and England maintained possession smartly at the line out before opening up play.
Smith was orchestrating deep inside the Springbok 22, with Henry Slade lobbing a super pass out to Manu Tuilagi, who dived over in the corner but hurt himself in the process - having already been heavily strapped up before kick-off - as Max Malins was called upon early.
Handre Pollard - returning to the South Africa starting lineup along with half-back partner Cobus Reinach and Sale lock Lood de Jager - got his side off the mark from the tee after Jonny May was left isolated inside the England 22, but the hosts quickly scored again.
Freddie Steward was sent forward into space by another stellar Slade pass. While the Leicester full-back and Jonny May were initially held at bay, Steward would not be denied as he eventually crashed over with green-and-gold shirted defenders draped all over him.
Pollard and Smith exchanged further penalties, with England’s coming after fine work from no8 Tom Curry that forced towering lock Eben Etzebeth into a breakdown infringement.
South Africa were comfortably second best, but the boot of Pollard - including one booming long-range effort from 55 metres - kept them in touch and meant they only trailed by five points at the interval, 17-12, with Smith failing badly with a late drop goal attempt.
The Springboks introduced their famed and refreshed ‘Bomb Squad’ early in the second half as momentum began to turn, though the previously reliable Pollard was off target with consecutive penalties as the South Africa scrum considerably turned up the heat.
Pollard’s next effort sailed through after Sam Underhill had his hands in the ruck, making it a two-point game with 25 minutes still to play.
England began to really lose their discipline as the penalty count kept ticking over and only some remarkable last-ditch defending from Malins kept Kwagga Smith from scoring.
Frans Steyn missed a drop goal attempt of his own before South Africa did take the lead for the first time through Elton Jantjies’ kick from the tee after England were whistled for offside.
But their one-point advantage did not last long as young Sale scrum-half Raffi Quirke - who replaced Ben Youngs with half an hour still to play in a big show of faith from Eddie Jones - sprinted clear to touch down after a fine break from Joe Marchant, set up by Slade.
It was a first England try for Quirke, 20, on only his second appearance.
Replacement prop Will Stuart was then punished for England’s persistent infringements as he was sent to the sin bin and South Africa quickly set about making their numerical advantage count, with their forwards battering through with the maul and narrowing the England defence before prolific wing Makazole Mapimpi went over in the opposite corner.
The extras were missed by Jantjies, though more England ill-discipline was punished by Steyn, whose penalty made it 26-24 to South Africa with just over five minutes left.
Etzebeth broke through for the Springboks but a rogue pass to Malcolm Marx halted a promising attack in its tracks, with captain Siya Kolisi then yellow carded for taking out Marchant in the air.
England’s opportunity for an upset looked to have gone after a pair of line out steals from Etzebeth, but two late South African infringements presented Smith the chance to secure a terrific win with seconds to spare - one he was never likely to pass up.