Flyhalf Sacha Feinberg-Mngomezulu and wing Kurt-Lee Arendse grabbed as brace each as flankers Siya Kolisi and Andre Esterhuizen, the latter moved from his usual centre position, prop Wilco Louw and centre Jesse Kriel also crossed for scores to go with a penalty try.
There would be no repeat of the there was no repeat of the ‘Miracle of Brighton’ a decade ago when Japan stunned South Africa with a 34-32 victory at the 2015 Rugby World Cup, considered one of the great upsets in rugby history.
Japan’s lone try came via fullback Yoshitaka Yazaki in a rare entry into the Springbok 22, but they could not cope with the physicality and precision of their opponents in difficult conditions.
"I thought we did what we wanted to do, we made a couple of mistakes but credit to Japan, they played with pace and moved the ball quickly," Springbok captain Kolisi said.
"We tried to slow it down at the breakdown and make our hits. We had to work for everything we got today."
South Africa applied pressure from the kick-off and Kolisi had their first try inside four minutes as the Springbok captain came up with the ball from a five-metre driving maul in his 99th test appearance.
Both sides opted for contestable kicks on attack rather than ball in hand in the slippery conditions, and it was from one of those that the Springboks scored their second try.
A Japanese clearance failed to find touch and Feinberg-Mngomezulu collected and hoisted the ball into the sodden sky, before collecting the ball from a Japanese fumble and crossing for the try.
Feinberg-Mngomezulu scored an excellent solo score for the Springboks’ third try as he ghosted into a gap and beat three defenders with his pace and power.
"He (Feinberg-Mngomezulu) was good, he is doing well and improving with each game," Kolisi said. "He has amazing coaching staff behind him and also people like Handre (Pollard) and Manie (Libbok) who are giving him great help.
"We are more focussed on the team effort, without the forwards he can’t do what he does. I am proud of the boys but we have to step up next week.”
Earlier in the movement prop Ox Nche was injured and the sight of him limping off will be of deep concern for coach Rassie Erasmus, such is his importance to their scrumming effort with France in Paris next week.
The fourth score was a penalty try as the springboks dominated the forward battle and their driving maul from a line-out was illegally sacked, with prop Shuhei Takeuchi receiving a yellow card for the infringement as South Africa led 26-0 at halftime.
Just as Japan were ready to welcome back Takeuchi from the sin-bin, they lost flanker Ben Gunter after head-on-head contact with Siya Kolisi in an illegal tackle that drew another yellow card.
Yet another break from Feinberg-Mngomezulu brought a fifth try scored by Louw, his first in test rugby.
Japan got on the scoreboard with a quick tap-and-go from Yazaki with a nice piece of quick thinking, but it was only a temporary reprieve.
Arendse crossed for South Africa’s sixth try though as Japan knocked a contestable kick back, but it was perfect for the wing to collect and score.
Hybrid centre/flanker came off the bench as a forward early in the second period and he was the latest try-scorer, barging his way over from another attacking lineout.
Cheslin Kolbe’s burst through a swath of Japanese defenders led to another score as his kick ahead was collected by Arendse, before Kriel's late try finished off the scoring.