Les Kiss was made to sweat in his Wallabies coaching debut as the visitors survived moments of calamity and a red card to beat Japan 35-32 in Osaka.
The visitors trailed early but, just as they appeared set to steady and surge away, were reduced to 14 men for 20 minutes thanks to a Miles Amatosero red card.
Japan, coached by Eddie Jones and seeking their first win in eight encounters, smelt blood.
But the Wallabies, while unconvincing, did enough in 30 degree heat to win a second-straight Test and first under new coach Kiss.
Japan led after a helter-skelter first 15 minutes, silky flyhalf Ryunosuke Ito slicing through staggered defence after Wallabies flanker Fraser McReight had won a penalty, tapped and run out of his defence only to turn the ball over with a speculative pass on halfway.
Harry Potter had an immediate reply though, the Wallabies going right then left before the winger ran back on the angle to score.
Flyhalf Declan Meredith continued to battle with his exit kicking, earning precious little ground to ensure Japan maintained the pressure.
But the visitors still slowly got traction, lock Josh Canham winning a penalty and Tom Wright the try-scorer after some rare fluency in attack.
They looked set to cross again from a driving maul in the right corner.
But the Japanese twisted it to a stop and Amatosero's rush of blood not only cost them the points, but gave Japan a numerical advantage for 20 minutes.
The lock, who has a reputation as a hot head after a preseason run-in with a NSW Waratahs teammate, had his left arm tucked when he attempted to clean out Japan captain Warner Dearns.
Dearns was moved by a tackler and Amatosero's shoulder appeared to hit the Hurricanes Super Rugby star in the head.
The yellow card was upgraded to a 20-minute red and it took Japan barely a minute to capitalise, opening up the Wallabies around the ruck and scoring through Faulua Makisi to lock it up at halftime.
Joseph-Aukuso Suaalii showed nice footwork and his offload set up a nice Wallabies try, Max Jorgensen barging over while the Wallabies were still down a man after the break.
The teams traded tries and then Japan took three points to make it a six-point game before the Wallabies were allowed their full contingent.
Fumbles kept Australia under the pump and Japan took another three to edge closer approaching the final quarter.
A penalty steadied them though and replacement prop Taniela Tupou easily burrowed over, under the posts, to stretch the lead to 10 with as many minutes to play.
Ben Donaldson entered the game at fullback, with Suaalii pushed to a wing when centre Isaac Henry became Wallaby No.999 with eight minutes remaining.
Japan weren't done though, winning a scrum penalty and peppering the line and Dearns finally crossing with two minutes to play.
The hosts had possession searching for the match-winner but spilt it in the final seconds to secure Australia an unconvincing win.