Their front row reserves were quickly called into action - Sona Taumalolo and Halani Aulika coming on for props Soane Tonga'uiha and Taufa'ao Filise after halftime and Aloisio Ma'asi replacing hooker and captain Aleki Lutui after 47 minutes.
Both sides were desperate to score their first win of the tournament and both would have targeted the other as a prime opportunity to score at least four match points.
With Kurt Morath, who didn't play against Canada, re-instated at first-five ahead of Taniela Moa, Tonga had a specialist pivot to guide them around the park.
Moa, back at halfback, is more suited to sniping close to the ruck and he has an eye for the gap, if not for himself then for his support runners.
Japan second-five Australia-born Ryan Nicholas caught the eye with his straight running, as did centre Alisi Tupualilai, who scored an outstanding try when running back against the angle to give Japan a glimmer of hope as the game entered the final quarter.
They were up against two sizeable centres in Alipate Fatafehi and Siale Piutau but more than held their own.
Japan were lucky to get away with the sinbinning of first-five James Arlidge in the first half. Arlidge was given 10 minutes by referee Pearson for a professional foul after being caught offside with half an hour gone.
Rather than concede any more points, Japan closed the gap thanks to fullback Shaun Webb, who took over the kicking duties to convert a penalty.
No8 Viliame Ma'afu scored for Tonga in the opening minutes, his try off the back of an attacking scrum ruled legal by the TMO Giulio De Santis of Italy just minutes after another effort was ruled out.
Japan scored a controversial equaliser after 14 minutes through Kensuke Hatakeyama, who burrowed over the line in a what looked suspiciously like a double movement. Referee Dave Pearson originally signalled a penalty for Japan, only to change his mind and go to the TMO, who quickly awarded the try.
Tonga lock Tukulua Lokotui took advantage of some lax defending on the blindside to reply straight away, Morath's conversion going over via the right upright.
Japan were in touble at scrum time, as Kirwan predicted, but their angled running and accurate passing had Tonga going backwards.
Michael Leitch was at the end of a brilliant Japan reply, the New Zealand-born flanker backing up well following thrusts by first Ryan Nicholas and then Shaun Webb to reach out and score.
Fullback Webb kicked Japan closer with two minutes remaining in the half.
After the break Morath kicked Tonga further ahead and wing Fetu'u Vainikolo scored in the corner to put his side in the box seat.
Morath played a key role for Tonga and kicked six from seven, his opposite James Arlidge, Japan's hero in the narrow defeat to France, had a disappointing match, missing all three of his kicks and failing to stamp his authority.
Tonga next play France in Wellington on October 1.
Tonga 31 (Viliame Ma'afu, Tukulua Lokotui, Fetu'u Vainikolo tries ; Kurt Morath 2 cons, 4 pens)
Japan 18 (Kensuke Hatakeyama, Michael Leitch, Alisi Tupualilai tries; Shaun Webb pen)
HT: 18-13