Aiden O'Neill, who was ill for that clash in Saitama, replaces Luke Brattan as Jackson Irvine's midfielder partner, in the only change to Popovic's line-up for Thursday night's game at AAMI Park.
Brattan is out of the squad altogether for games against Saudi Arabia and Bahrain, who Australia play away in Riffa on Wednesday morning AEDT.
Popovic appears to be sticking to his back three with wingbacks, with Jordy Bos again preferred over Aziz Behich on the left.
Mitch Duke retains his starting striker spot ahead of the returning Kusini Yengi,Â
With Craig Goodwin suspended, the Socceroos can't count on the slick left-footer's set pieces to break the contest open, while Martin Boyle and Hayden Matthews have been left out.
Irvine will once again skipper the Socceroos with captain Mat Ryan again benched for fellow goalkeeper Joe Gauci.
The game, and the following away match against Bahrain, couldn't be more pivotal to Australia's hopes of direct qualification for 2026.
Japan (10 points) are outright Group C leaders with Australia (five points, +1) ahead of Saudi Arabia (five points, -1) and Bahrain (five points, -4) on goal difference.
The top two teams in group C secure direct qualification for the 2026 World Cup while third and fourth place go into the next round of qualifying.
SOCCEROOS STARTING LINE-UP
Joe Gauci (GK); Lewis Miller, Jason Geria, Harry Souttar, Cameron Burgess, Jordy Bos; Aiden O'Neill, Jackson Irvine; Ajdin Hrustic, Riley McGree; Mitch Duke.
9°C