'The Beast' Mtawarira upended Keita Inagaki midway through the first-half and was sin-binned for the crude tackle.
But referee Wayne Barnes reached immediately for a yellow card, opting not to refer the decision to Television Match Official (TMO) Rowan Kitt.
Inagaki landed on his head, leaving Japan frustrated with the level of punishment delivered to Mtawarira.
So just when Japan thought they could shock the rugby world for a third time in five weeks the Springboks rolled up their sleeves and flexed sufficient muscle to subdue Jamie Joseph's men.
Where Japan conjured the miracle of Brighton by edging out South Africa 34-32 in 2015, here on home turf the Brave Blossoms fell prey to a brutalising by the Boks.
The world's newest favourite team found precious few answers when South Africa stuck the ball up their jumper, killing the game with a rampant driving maul for De Klerk's try.
Japan might have downed Ireland 19-12 and ploughed past Scotland 28-21, but the hosts wilted in the Southern Hemisphere onslaught.
Now the Boks will face Warren Gatland's Wales in Yokohama on Sunday, in a bid to reach their first final since 2007.
The tournament burst into life with a breathless group stage encounter between South Africa and New Zealand, that the back-to-back world champion All Blacks won 23-13.
There remains every chance the World Cup could finish just as it began then, with both South Africa and New Zealand appearing dangerous in attack and resolute in defence.
Japan ultimately never recovered from a horror-show start.
The Boks exposed Tamura defending blindside from a scrum, and left the fly-half with nowhere to hide.
De Klerk fed Mapimpi and the powerful wing stormed over the top of Japan's playmaker and over the line for a near-immediate opening score.
Japan recovered and dominated possession throughout the first-half, but could not find a way onto the scoreboard barring a penalty for Tamura.
Not even Mtawarira's yellow card and a 10-minute one-man advantage could help Japan find a chink in the Springboks' hugely-impressive defensive armour.
Fukuoka is due to retire after the World Cup to seek a career in medicine, but the 27-year-old boasts the fastest feet in the Far East and would be a huge loss to the world game should he hang up his boots prematurely.
South Africa could only take a 5-3 lead into the interval but eventually ground down the hosts after that break.
Pollard slotted three from four penalty attempts as Rassie Erasmus' side inched their way to victory.
And when De Klerk scampered over after that stunning driving maul, the match was over with a quarter-hour still on the clock.
Mapimpi still had time to blast clear and home for his second of the night, to close the game in style.
And so Japan's adventure came to a gruelling close not befitting with the audacious attacking elan that so lit up this tournament.
But even in defeat they can hold heads high and look to a big future.
The Boks meanwhile will be very seriously eyeing a third world title.