Ange Postecoglou's team selection in Saitama has come under further pressure after Japan revealed the controversial decision gave them a boost during Thursday's World Cup qualifier.
The Socceroos boss chose to start Robbie Kruse as a lone striker, with Tim Cahill and Tomi Juric used off the bench in the second half, while Aaron Mooy wasn't in the squad because of illness.
Despite dominating possession, the green-and-gold failed to create many clear-cut openings, with the Blue Samurai clinically taking their opportunities in a 2-0 victory that earned an automatic World Cup berth.
Defender Maya Yoshida explained his shock at seeing the Australian team sheet pre-match and said the away side couldn't find an answer to Japan's sturdy defence.
"I'm a little bit surprised because there was no Mooy, Juric and Cahill. It helped us a little bit more than we expected," the Southampton centre-half said.
"I think we defended very well and they struggled to bring the ball up, especially when their three backs had the ball. They tried to find the solution but they couldn't."
Mooy faces a race against time to recover from his illness before the Socceroos meet Thailand in Melbourne on Tuesday - a must-win match before the nation's fate rests with the contest between Saudi Arabia and Japan on Wednesday (AEST).