The Springboks ended England's remarkable assault on world title glory by landing the Webb Ellis Trophy for a second time in 12 years.
But England, 80-1 no-hopers after losing 36-0 to South Africa in the pool stages 36 days earlier, made them fight every inch of the way.
And they could feel aggrieved at the final scoreline, given that wing Mark Cueto saw a 43rd-minute corner try not awarded by the video referee, while Springboks centre Francois Steyn's penalty clincher came after a dubious decision for obstruction.
In the end though, not even Jonny Wilkinson could complete England's mission improbable against a South African side - brilliantly coached by Jake White - that fulfilled what they always felt was their destiny.
Full-back Percy Montgomery kicked four penalties, while Wilkinson booted a double for England, yet their hopes of becoming the first country to successfully defend the World Cup ultimately floundered.
it was a typically resilient England performance though, despite them ending the final with reserve scrum-half Peter Richards in the back-row after substitute flanker Joe Worsley went off injured.
England fielded four survivors from their 2003 World Cup final starting line-up - Wilkinson, skipper Phil Vickery, lock Ben Kay and full-back Jason Robinson, who played his 51st and final Test match before retirement.
South Africa, meanwhile, had one World Cup winner - prop Os du Randt - who was a member of their successful 1995 campaign on home soil.
The Paris temperature plummeted as kick-off approached, but conditions were perfect, given a firm pitch and little wind to affect goalkickers.
And England made a promising start, putting immediate pressure on South Africa's back three through some steepling kicks, but the Springboks took a seventh minute lead when Montgomery slotted a penalty after centre Mathew Tait slipped inside his own 22 and then failed to release possession.
Wilkinson drew England level five minutes later, finding his range from the touchline, yet Montgomery continued the game's nip and tuck nature by landing his second penalty after England flanker Lewis Moody needlessly tripped Springboks fly-half Butch James.
Bath-bound James then tested England's defence with a neat chip and chase, but only after Wilkinson had arrowed an angled drop-goal attempt wide and Steyn drifted a long-range penalty attempt narrowly off target.
South Africa's renowned power game finally surfaced as half-time approached as they laid siege to England's line.
But the defending champions, epitomising the collective spirit that had taken them into a second successive final, refused to budge an inch.
Some ferociously-committed tackling kept the Springboks out when it looked certain as though they would score.
Montgomery though, who had his right knee bandaged after being on the receiving end of a crunching collision seconds earlier, stepped up to complete his penalty hat-trick with the final kick of an enthralling opening period.
Montgomery's strike took him past 100 points for the tournament, and trailing 9-3, England needed to regain a territorial foothold.
But Vickery, who appeared to take a couple of heavy blows to his left shoulder, did not reappear for the second half. He was replaced by Bath prop Matt Stevens, with flanker Martin Corry taking over leadership duties.
There was an embarrassing incident for tournament organisers when a spectator ran on to the pitch within a minute of the restart.
The real drama though, came just 60 seconds later as England looked to have forged ahead.
Tait made a brilliant 40-metre break from just inside South Africa's half, and with the Springboks' defence retreating, England recycled possession brilliantly, and Wilkinson's superb flick-pass looked to have put Cueto over.
But the television match official - Australian Stuart Dickinson - had other ideas after a lengthy delay, deciding Cueto's knee grazed the touchline as he dived over.
Cueto's agonising shake of his head after the decision told its own story, yet Wilkinson kicked an immediate penalty, narrowing the gap to 9-6.
England saw Robinson limp off on 47 minutes - he failed to last the pool game against South Africa because of a hamstring injury - and Leicester centre Dan Hipkiss replaced him, with Tait switching to full-back.
It was a demoralising end to Robinson's England career, even though he would have been lifted by the ensuing standing ovation.
Montgomery and Steyn then slotted the kicks that ended England's reign as world champions, with South Africa counting down the clock in expert fashion and the men in white offering little attacking threat.