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The Australians simply had too much strike for the home side though, running in nine tries in an assured 33-point victory.
Tevita Kuridrani scored a hat-trick, while his centre partner Samu Kerevi got a double in a clash where the Wallabies were never seriously threatened by the Japanese side and produced some spectacular attacking Rugby.
After leading 35-3 at the end of a completely dominant opening half, Wallabies skipper Michael Hooper lamented his side's final 20 minutes.
"It was a really hard, fast game and it was hot out there early on. We were really happy with about 60 minutes of our game but we conceded those points late and we've got to be better than that," said Hooper.
"Well played to Japan. It was a great experience playing here. The fans were loud and you can feel how big its going to be here in two years time for the World Cup."
Stand-in fyhalf Reece Hodge was outstanding in his debut in the Wallabies number 10 jersey, directing traffic and knocking over a perfect nine-from-nine with the boot. Sean McMahon continued is strong season in the gold jersey and Kurtley Beale was again instrumental in attack in his new role from fullback.
It was Beale's cut-out pass that sent Kerevi over for his first to open the scoring in the 6th minute, then Hodge who found Speight on his inside for the second Wallabies try five minutes later.
Tatafu Polota-Nau then crashed over from a maul, and Kuridrani capitalised on a powerful run from McMahon to snare his first five-pointer in the 33rd minute. As the siren sounded for half time, Kuridrani dotted down again as he chimed in on an inside ball from winger Marika Koroibete.
Japan came out full of running to start the second stanza, and it was replacement backrower Wimpie van der Valt who eventually found the tryline. But three more strikes by the Wallabies, including a spectacular effort from Samu Kerevi snuffed out any hope of the home side mounting a challenge.
The Brave Blossoms kept up the fight though, and rewarded their energetic fans with two tries in the final 10 minutes through Melbourne Rebels import number eight Amanaki Mafi, and Kazuki Himeno.