The 'Ikale Tahi led 16-11 at halftime, despite skipper Nili Latu being sent to the sin-bin for infringing at the breakdown, and scored tries through Halani Aulika, Fetu Vainikolo and man of the match Sonatane Takalua, with Kurt Morath adding 16 points from the boot.
It was Tonga's third win in a row, and fourth in succession against Japan.
Tonga Rugby's High Performance Manager, Peter Harding, says the result was all the more satisfying as they were missing some key players.