Cheslin Kolbe, the other Springboks wing, scored two tries and replacement scrumhalf Herschel Jantjies added the final try when he ran more than 50 meters in the last minute to maintain his impressive start to internationals.
Jantjies has scored four tries in his first four tests. Kolbe touched down for the first try in the seventh minute and Japan trailed 22-0 at halftime at Kumagaya Rugby Stadium, meaning it was never in position to repeat one of the biggest surprises in test rugby when beating the Springboks at the 2015 World Cup.
Kotaro Matsushima scored Japan's only try after an hour, capitalizing on a Springboks backline error, but Mapimpi had completed his hat trick by then. South Africa was 27-0 up before Japan got on the scoreboard.
Japan opens the Rugby World Cup against Russia in Tokyo on Sept. 20. It's the first non-traditional rugby nation to host a World Cup and Japan had built up to the occasion with some promising recent results.
Japan, coached by former New Zealand loose forward Jamie Joseph, beat Fiji, Tonga and the United States to win last month's Pacific Nations Cup. Japan, however, couldn't handle the resurgent Springboks, who won the Rugby Championship and have been revitalized under coach Rassie Erasmus. South Africa's first game at the World Cup is against two-time defending champion New Zealand a day after Japan's tournament opener.
The bigger Springboks impressed their forward dominance on Japan in Kumagaya, where nearly 30,000 people watched at one of the World Cup venues. Kolbe's opening score in the right corner and Mapimpi's first in the left corner both came from strong Springboks scrums.
With Japan reluctant to put the ball out and engage in a set-piece battle, Springboks fullback Willie le Roux caught a misdirected kick from Japan flyhalf Yu Tamura and set Mapimpi clear for his second try in the 31st.
Mapimpi sped away on an overlap for his hat trick early in the second and Kolbe intercepted to go nearly the length of the field. South Africa's last two tries, through Kolbe and Jantjies, came in the final 10 minutes while the Boks were down to 14 men with replacement loose forward Francois Louw in the sin bin.
Japan wing Matsushima's breakaway avoided the home team being kept scoreless in its final warmup, but Joseph's task was made clearer by the defeat. He must find a way for Japan to play its skillful, fast-paced game against bigger, stronger forward packs at the World Cup. Ireland, Scotland and Samoa are also in the host's pool and only two teams qualify from each pool for the quarterfinals.
Japan has never got past the pool stage at a World Cup despite playing in every edition.
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