Early tries from number eight Vili Ma'afu and lock Lua Lokotui gave Tonga an early lead, with a further try from wing Fetu'u Vainikolo and 16 points from the boot of fly-half Kurt Morath sealing the victory.
Japan hit back with tries from prop Kensuke Hatakeyama, flanker Michael Leitch and centre Alisi Tupuailei, plus a penalty from Shaun Webb, but they paid the price for being unable to consistently match the physicality of their opponents and slumped to their third-straight defeat.
Japan made an awful start as their efforts to attack from deep inside their 22 saw number eight Takashi Kikutani gift Tonga early field position with a knock-on.
Scrum-half Taniela Moa was denied by the video referee, but the same official replied in the positive as Ma'afu crashed over to give the South Sea Islanders a 5-0 lead.
Japan instantly hit back as breaks from centre Tupuailei and Kosuke Endo laid the foundations for Hatakeyama to burrow over and level the scores.
But parity lasted barely a minute as Japan failed to hold the restart and Lokotui was given a simple run-in, courtesy of a suspiciously forward pass, with Morath adding the tough conversion via an upright.
The game's fourth try arrived after just 24 minutes as Japan centre Ryan Nicholas made the initial cut in midfield for flanker Leitch to get over out wide for another unconverted try.
Morath kicked two penalties to give Tonga an 18-10 lead, with the latter of those three-pointers seeing Japan fly-half James Arlidge sin-binned for a cynical offside, but Shaun Webb replied with a penalty of his own just before the interval.
Despite Arlidge's return from the bin Tonga controlled the early stages of the second stanza, with Morath knocking over his third penalty to re-establish an eight-point lead.
And Isotolo Maka's side gave themselves further breathing space after 55 minutes when they made the most of a lucky ricochet in midfield to work impressive wing Vainikolo over on the right, with Morath once again on target with the extras.
But having opened a handy gap the Islanders gave Japan a route back into the game as replacement Halani Aulika was binned, and their opponents took advantage as Tupuailei's fine angled run took him over, although Arlidge failed with a third-straight conversion attempt.
But yet another Morath penalty ensured a comfortable win for Tonga, despite Lokotui's late yellow card.
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