It was the Boks' 23rd Test hat-trick and the first since Bryan Habana crossed for three tries against the USA at the Rugby World Cup in London in 2015.
Mapimpi dotted down in the 24th, 31st and 52nd minutes as the Boks played well in patches of the match. Cheslin Kolbe scored two more tries for South Africa, while Herschel Jantjies dotted down at the end of a comprehensive victory.
While the performance was all but perfect, the Boks will still be happy with their defence, set piece play and aerial skills. Rassie Erasmus said afterwards the Boks achieved what they set out to do.
The Bok defence was especially good - they made nearly 200 tackles as they managed to keep the Japanese out on numerous occasions where the hosts applied long periods of pressure deep in the South African half.
Playing in his 50th Test for South Africa, the Boks' defensive charge was led by the impressive Pieter-Steph du Toit, but all the players deserve applause for the way in which they limited the hosts' room to move.
Japan’s only try, by South African-born winger Kotaro Matsushima, came after an hour, and from a Springbok backline move that went awry.
And while it was a night for the wings, Mapimpi was the one who made the biggest impact. His first try came after Willie le Roux masterfully gathered a high kick by Japan, his second was the result of a devastating scrum and quick hands by the Boks, and his third from broken play, with good handling again a vital ingredient in the success of the move.
Despite being in control on the score board, the Boks never relaxed on defence, as was evident with Kolbe’s second try, in the 72nd minute. The visitors applied defensive pressure with the hosts hot on the attack in the South Africa 22, and the speedy winger gratefully intercepted a forced pass and ran 90m to score under the uprights.
Herschel Jantjies continued with his dream debut season in the green and gold when he took the ball from broken play, saw no Japanese defender in front of him and ran 60m to score his fourth Test try.
Rassie Erasmus gave all of his players game time in the match, with Frans Steyn taking over at flyhalf from Handre Pollard, while Trevor Nyakane was forced to leave the field with an injury. Francois Louw was yellow carded in the 71st minute for repeat offences.
Japan (0) 7 – Tries: Kotaro Matsushima. Conversion: Yu Tamura.
Springboks (22) 41 – Tries: Cheslin Kolbe (2), Makazole Mapimpi (3), Herschel Jantjies. Conversions: Handré Pollard (2), Frans Steyn (2). Penalty goal: Pollard.