The 40,000-strong crowd came alive early in the second half when South African- born lock Wimpie van der Walt scored on debut, with a penalty goal soon after by Rikiya Matsuda boosting their tally by 10.
But after some strong lead-up work by Henry Speight, Samu Kerevi galloped away for his second of the day to stall Japan's momentum.
Australia's forwards deserved credit for the try-scoring spree, with hooker Tatafu Polota-Nau, flanker Sean McMahon and try-scoring lock Rob Simmons among their best.
Japan's rookie lock Kiazuki Himeno scored at fulltime, while their Melbourne Rebel back-rower Amanaki Mafi, who last month was named Australia's Super Rugby player of the year, was also rewarded with a late try.
The margin meant the Wallabies were able to empty their bench, giving lock Matt Philip his debut, and their starters some extra rest before taking on Wales next Saturday followed by Tests against England and Scotland.