The host nation took the tournament by storm after winning all its group stage games but was overpowered by a physical South African side in Sunday’s quarterfinal clash.
A fourth-minute try from Makazole Mapimpi gave the Springboks an early lead before Japan came back strongly and were rewarded with a penalty from Yu Tamura.
A closely-fought first half ended 5-3 — the lowest-scoring first 40 of the tournament so far — but it was a different story after the break.
Three penalties from Handre Pollard saw South Africa extend its lead as its big forward pack began to take control of the game.
Faf de Klerk got his side’s second try after a rolling maul that had surged into the Japanese half and Mapimpi’s second try — his fifth of the tournament — took the game out of sight.
The Springboks next face Wales, which beat France 20-19 in Sunday’s other quarterfinal, in the final four.
More to follow.