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Japan had set their home tournament alight with a scintillating style of organised chaos that swept them through their pool unbeaten with victories against tier one nations Ireland and Scotland.
Their fairytale run, however, ended against a formidable Springboks defensive effort that slowed the Japanese speed, while the South Africans, who only led 5-3 at halftime, relied on halfback pairing Faf de Klerk and Handre Pollard to keep them pinned in their own half.
The Springboks, who scored three tries - two from winger Makazole Mapimpi - but wasted a string of other chances, will now face Wales in the semi-finals in Yokohama next week after they recorded a 20-19 victory over a 14-man France, who had lock Sebastian Vahaamahina sent off at Oita Stadium earlier on Sunday.