The Japanese, known as the Brave Blossoms, trailed France by four points with less than 15 minutes left before losing 47-21 in their first match. Keeping an eye on Tonga, Kirwan then rested his best players, and his revamped side lost 83-7 to the All Blacks.
Kirwan's pre-tournament target was to record two victories, seemingly a modest aim until one realises Japan entered with just one win in 20 matches from all six previous World Cups and that was against Zimbabwe 20 years ago.
But the team's form and depth have steadily improved, culminating in victories over Tonga and Fiji en route to winning the 2011 Pacific Nations Cup, a tournament that also included Samoa.
"We watched them on film but they play a real simple game. We've figured out their strengths as well as their weaknesses," Japan flanker Itaru Taniguchi said of Tonga.
"We're not just going to try to stop them, we're going to hit back. My guess is that they think Japanese players will sit there and take it, so imagine how surprised they might be if we took it right to them."
The Tongans were beaten 41-10 by New Zealand in the tournament opener, then made 12 changes in a 25-20 loss to Canada that realistically ended their bid to make the quarter-finals.
Both teams have largely reverted to their first-choice players, and stand-in Tonga captain Aleki Lutui feels the burden of expectation.
"It's a game that we need to win, so it's a big responsibility when you get called up to be captain," said Lutui, who takes over the role in place of the injured Finau Maka.
"We are disappointed with Canada and before that, the All Blacks. Now we have to get it right. There is a lot of people to play for. Not just us, but our supporters."
Kirwan feels conditioning will be crucial and praises Tonga coach Isitolo Maka's role in the Pacific islanders' improvement.
"I think Isitolo's done a great job, we've certainly seen progression through the last few PNCs when Isi's been involved. We are really happy with our fitness, too. I think that it could come down to fitness."
Japan captain Takashi Kikutani took a lot out of the squad's visit to Tane Mahuta but wasn't sure if he would be able to call on its magic tonight.
"I'm really glad I went ... I feel like I've been given a spiritual lift by the tree," he said.
"But the bus ride back to our hotel was really rough. I couldn't sleep because the driver was going so fast up a mountain on twisting, winding roads. I probably used up all the healing power I got from the tree on the ride back."
Tonga - Japan, Whangarei. Tonight, 7.30