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Sixteen points from the boot of Tongan flyhalf Kurt Morath made the difference as Japan slumped to their 17th consecutive World Cup defeat and failed in their bid to win two games at this tournament.
Tonga had the better of a helter-skelter first half 18-13 and they attacked from the kick-off when scrumhalf Taniela Moa was held up just inches short in the first attack of the game.
Viliami Ma'afu crossed the line minutes later but replays showed he was held up by some desperate Japanese defending. But the video referee had no problem with Ma'afu's second effort when he picked up and charged over from a five metre scrum.
Japan hit back when wing Kosuke Endo made a clean line-break and prop Kensuke Hatakeyama mauled his way over the line in the 13th minute.
But again from the kick-off, Tonga had a simple score when they secured their own ball and from a ruck, secondrow Tukulua Lokotui was released for a simple score on the left.
Alisi Tupuailai nearly ran the length of a pitch for an intercept try before being tackled but Ryan Nicholas then broke to set up Japan's second score when Michael Leitch came on to an inside pass on the right wing and barged through a wall of defenders.
Tonga's Morath kicked a penalty from 22m and another when Japan's goal-kicking flyhalf James Arlidge was sin-binned for offside.
But they were unable to make the numerical advantage count and it was Japan's stand-in kicker Shaun Webb who coolly kept the Brave Blossoms in touch 13-18 with a penalty close to half-time.
Morath knocked over a penalty shortly after the break and Fetu'u Vainikolo provided the killer blow with a brilliant finish from the right wing for Tonga's third try.
Samoan-born Alisi Tupuaili kept Japanese hopes alive when he gathered a crossover pass and scored on 63 minutes, but some more last-ditch attacking from the Brave Blossoms could not prevent the stinging defeat.
Tonga, currently ranked 15, have won five of their 12 games against Japan but they last beat the Brave Blossoms way back in 2006.
Japan's final game is against Canada in Napier next Tuesday while Tonga play France in Wellington on October 1.
Teams:Tonga:
15 Vungakoto Lilo, 14 Fetu'u Vainikolo, 13 Siale Piutau, 12 Alipate Fatafehi, 11 Sukanaivalu Hufanga, 10 Kurt Morath, 9 Taniela Moa, 8 Viliami Ma'afu, 7 Sione Vaiomo'unga, 6 Sione Kalamafoni, 5 Paino Hehea, 4 Tukulua Lokotui, 3 Taufa'ao Filise, 2 Aleki Lutui (captain), 1 Soane Tonga'uiha
Substitutes: 16 Aloisio Ma'asi, 17 Alisona Taumalolo, 18 Halani Aulika, 19 Joseph Tu'ineau, 20 Samiu Vahafolau, 21 Samisoni Fisilau, 22 Viliame Iongi
Japan:
15 Shaun Webb, 14 Kosuke Endo, 13 Alisi Tupuailai, 12 Ryan Nicholas, 11 Hirotoki Onozawa, 10 James Arlidge, 9 Fumiaki Tanaka, 8 Takashi Kikutani (captain), 7 Michael Leitch, 6 Itaru Taniguchi, 5 Toshizumi Kitagawa, 4 Luke Thompson, 3 Kensuke Hatakeyama, 2 Shota Horie, 1 Hisateru Hirashima
Substitutes: 16 Yusuke Aoki, 17 Nozomu Fujita, 18 Hitoshi Ono, 19 Sione Talikavili Vatuvei, 20 Atsushi Hiwasa, 21 Takehisa Usuzuki, 22 Murray Williams