However, Lutui's men held on with the Tongans' physicality and fly-half Kurt Morath's superior place kicking proving the difference.
The victory, in front of thousands of members of New Zealand's Tongan community, follows Tonga's brave defeat to New Zealand and bitterly disappointing loss against fellow minnows Canada.
"Today we tried to get it right," said captain Lutui. "I'd like to thank the supporters, they mean a lot to us. Last week they were disappointed, now we've given them something to cheer."
Japan: Shaun Webb, Kosuke Endo, Alisi Tupuailai, Ryan Nicholas, Hirotoki Onozawa, James Arlidge, Fumiaki Tanaka; Takashi Kikutani (captain), Michael Leitch, Itaru Taniguchi, Toshizumi Kitagawa, Luke Thompson, Kensuke Hatakeyama, Shota Horie, Hisateru Hirashima. Replacements: Yusuke Aoki, Nozomu Fujita, Hitoshi Ono, Sione Talikavili Vatuvei, Atsushi Hiwasa, Takehisa Usuzuki, Murray Williams.
Tonga: Vungakoto Lilo, Fetu'u Vainikolo, Siale Piutau, Alipate Fatafehi, Sukanaivalu Hufanga, Kurt Morath, Taniela Moa; Soane Tonga'uiha, Aleki Lutui (captain), Taufa'ao Filise, Tukulua Lokotui, Paino Hehea, Sione Kalamafoni, Sione Vaiomo'unga, Viliami Ma'afu. Replacements: Aloisio Ma'asi, Alisona Taumalolo, Halani Aulika, Joseph Tu'ineau, Samiu Vahafolau, Samisoni Fisilau, Andrew Ma'ilei.