Once again playing with just ten on the roster, the Opals exploded out of the gate with a 32-23 opening term but their offence dried up in the second period as Japan pulled themselves back into the contest.
The second half was an arm-wrestle before Australia's hot shooting carried them over the line as they hit 58% from within the arc compared to Japan's 46%.
"Tonight was a very high level game," said Opals coach Brendan Joyce.
"We expected them to be extremely physical after being 0-2 down and that is what we got.
"I thought our players did a great job playing through contact and finishing the game strong in the fourth quarter."
With 26 points, Liz Cambage again top-scored for the contest, shooting 10-14 from the field to go with seven rebounds, three steals and three blocks.
Leilani Mitchell starred in the back-court, hitting three three-pointers for 19 points, three rebounds and three assists while Suzy Batkovic also reached double-figures with 13 points and Steph Talbot tallied eight points and five assists.
Ahead of August, the Opals will now head to Europe for a two-week tour of warm-up games in late May-early June before returning home for two final camps in June and July.