Halani Aulika, Fetu'u Vainikolo and Sonatane Takulua all crossed over for the Tongans, with Hendrik Tui scoring Japan's only try.
Japan led 6-3 following two penalties from Ayumu Goromaru, before Aulika's 30th minute try was converted by Kurt Morath to give Tonga a 10-6 lead. However, Tui responded to put Eddie Jones's side momentarily back in front.
