The Wallabies held on after a nerve-jangling finale to set themselves up for their trip to Europe, where they will face England, Italy, Ireland and France on successive weekends.
Nick Champion de Crespigny, captaining the team in just his third international appearance, scored Australia’s first try before Josh Flook added another before half-time.
Japan hit back after the break through Shuhei Takeuchi before Carlo Tizzano scored another try for the visitors.
Australia-born Japan flanker Ben Gunter brought the home side within four points midway through the second half but the Wallabies escaped with the win.
“I don’t think it needed to be that tense,” said Australia coach Joe Schmidt. “They kept working their way back.
“It was wet tonight, very difficult conditions. You would have seen a pretty high error rate from both teams just because the ball was slippery.”
Schmidt fielded a new-look team with 13 changes from the side that lost to New Zealand this month.
Both teams were forced into early changes, with Australia’s Lukhan Salakaia-Loto and Japan’s Shogo Nakano leaving the field within the first 10 minutes.
Australia took the lead minutes later when Champion de Crespigny pounced for a try after a penalty dangerously close to the Japan line.
A yellow card for Japan’s Charlie Lawrence left the home side temporarily short-handed and there was more injury woe for Australia when Josh Canham went off following a heavy hit.
Lee Seungsin kicked a penalty to get Japan on the board but Australia scored their second try minutes later.
A nicely worked move sent Andrew Kellaway running through the Japan defence and he fed Flook to canter over the line.
Japan looked livelier in the second half and Takeuchi scored their first try in the 52nd minute after a period of pressure.
Australia hit back five minutes later when Tizzano rumbled over for their third try. (AFP)
