Experienced outside backs Harry Potter and Tom Wright crossed for the Wallabies in a tied first half, while Japan scored tries through flyhalf prospect Ryunosuke Ito and powerful number eight Faulua Makisi.
Winger Max Jorgensen, flanker Fraser McReight and replacement Taniela Tupou added to Australia’s tally after the break, while tries from Japan flyer Kazuma Ueda and captain Warner Dearns, and two penalties from fullback Takuro Matsunaga, ran the match to the end.
"That was tough, wasn't it? Not just the conditions," said Kiss. "They're a good team. They play fast and hard at home in their backyard.
"Probably offered a few too many opportunities for them. We'll have a look at it. But overall, that's a test win. Well done, boys."
Japan’s rookie playmaker Ito, elevated by their Australian coach Eddie Jones from university rugby straight to the national team, opened the scoring with a piece of individual brilliance, jinking past three defenders to touch down under the posts.
But the Wallabies hit straight back with winger Potter eventually capitalising on some sloppy Japanese handling to scythe infield and score.
After the much-needed early water break in the stifling conditions, Australia started to turn the screw. The forwards pressed their physical advantage and the backs worked the ball wide allowing fullback Wright to find space to score.
The Wallabies looked likely to add to their tally before lock Miles Amatosero was given a 20-minute red card for a high tackle on his opposite number Dearns.
Japan immediately capitalised on the numerical advantage, with powerful No.8 Makisi shrugging off defenders on his way to a converted try that brought the scores level before halftime.
With the teams revitalised, the match began to open up with three tries within eight minutes of the restart.
First, it was 14-man Australia who pulled out some slick offloads to allow wing Max Jorgensen to wriggle over.
Brave Blossoms flyer Kazuma Ueda hit back, finding a weak shoulder and racing through a gap to score. Then Australia flanker Fraser McReight piled over back down the other end.
Japan’s Matsunaga became the first kicker from either side to miss the mark with his conversion but he quickly redeemed himself with two penalty goals.
As the match tightened up in the final quarter, Australia showed composure to eventually break down Japan’s dogged defence, allowing replacement Taniela Tupou to power over.
Japan refused to give up and after being camped on the Australian line for several phases, captain Dearns managed to burrow through a pile of bodies to find the whitewash, though his side would fall just short.
"We let ourselves down with a few fundamental errors in the last 20 minutes when we had an opportunity to probably put Australia away, so pretty disappointed, mate," said Jones.
"But yeah, I'm really proud of how hard the players are playing and there's a lot of development in this team."