The Socceroos also had to deal with an untimely hiccup, their team bus arriving at the ground only 45 minutes before kick-off at Saitama Stadium on Tuesday night after being caught in traffic due to an accident.
The Socceroos are attempting to claim their first-ever win over the Samurai Blue in Japan, after last beating the group C leaders in Melbourne in 2009.
Brattan, 34, replaces the unavailable Aiden O'Neill as Jackson Irvine's defensive midfield partner for Tuesday night's game - somewhat surprisingly ahead of Keanu Baccus.
Intriguingly, Goodwin, who had a goal and assist in last week's 3-1 win over China, drops to the bench along with Nestory Irankunda for dynamic duo Riley McGree and Ajdin Hrustic.
Craig Goodwin goes to the bench after his starring role against China. (Matt Turner/AAP PHOTOS)
Popovic has stuck with his back three formation, but made a plethora of changes to the make-up of his defence.
Cam Burgess and Jason Geria will sit on the left and right sides of Harry Souttar respectively, chosen ahead of Kye Rowles and Thomas Deng.
Young gun Jordy Bos has replaced Aziz Behich at left wing-back, clearly to give more run and explosive power down the flank, while Lewis Miller is on the right side.
Joe Gauci has retained the starting goalkeeper spot ahead of Mat Ryan, with Irvine to wear the captain's armband.
Japan coach Hajime Moriyasu made two changes to his starting line-up.
Leeds United's Ao Tanaka and Real Sociedad's Takefusa Kubo replace Liverpool's Wataru Endo and Crystal Palace's Daichi Kamada.
Endo is not in the squad at all.
SOCCEROOS STARTING LINE-UP AGAINST JAPAN
Joe Gauci (GK); Jason Geria, Harry Souttar, Cameron Burgess; Lewis Miller, Jordy Bos; Luke Brattan, Jackson Irvine (C); Ajdin Hrustic, Riley McGree; Mitch Duke.
