Goals to Yasuyuki Konno and Shinji Okazaki in a seven-minute period in the second half had the hosts in control before Tim Cahill haunted Japan again with a trademark header in stoppage time.
But it was too little too late for Australia whose wait for a first win in Japan will go on and leaves coach Ange Postecoglou with a few things to ponder ahead of January’s tournament on home soil.
It was a mixed night for the Socceroos, who looked superb in the first half as they dominated the hosts in almost every department.
But they couldn’t maintain the same intensity and quality after the break, with Japan’s big-name stars coming to the fore to claim bragging rights before they head Down Under in less than two months.
Postecoglou made six changes to the starting XI that were beaten by Qatar last month, including starting Tim Cahill on the bench and playing Mathew Leckie, James Troisi and Robbie Kruse in a speedy front-three.
The visitors made a fast-start with Troisi and Leckie both flashing chances wide inside the first 10 minutes.
Enjoying the cooler conditions than what they encountered in the Middle East last month, the Socceroos took the game to Japan with some slick passing and measured build-up play.
Only a superb full-stretch save by Eiji Kawashima on 17 minutes kept the home side on level terms, keeping out Leckie’s powerful header from Massimo Luongo’s looping cross.
It’s just what Postecoglou would have wanted from his side, who were dominating possession while Alex Wilkinson and Trent Sainsbury were assured at the back.
Japan’s best – and only real - chance of the half came five minutes from the break, Shinji Kagawa getting to the byline and cutting the ball back, with skipper Mile Jedinak getting in a timely interception to stop what would have been a certain goal to Shinji Okazaki.
Untroubled for much of the opening 45 minutes, Socceroos goal-keeper Mat Ryan had to pull off two smart saves to deny both Kagawa and Okazaki within a couple of minutes at the start of the second half.
Substitute Takashi Inui, who had just come onto the pitch two minutes earlier, then let Australia off the hook on the hour mark when he headed over from close range.
It was a let-off for Postecoglou’s troops but one they didn’t head as Konno was left unmarked at the back post from a corner,
It’s the second goal Konno has scored against the Socceroos to go with his effort in a World Cup qualifier in Brisbane in 2012.
Okazaki made it 2-0 midway through the half, turning home Masato Morishige’s centre with a classy flick through his legs from just a few yards out.
Cahill was introduced with 17 minutes left and got his fifth goal against Japan, rising high to head home Aziz Behich’s centre at the death to halve the deficit but the home side held on for a well-deserved victory.
The defeat leaves the Socceroos with just one win for 2014 and some work to do ahead of the Asian Cup.
Japan: Eiji Kawashima, Masato Morishige, Kosuke Ota, Maya Yoshida, Gotoku Sakai, Makoto Hasebe, Yasuhito Endo (Yasuyuki Konno 46’), Shinji Kagawa, Shinji Okazaki (Yohei Toyoda 77’), Keisuke Honda, Yoshinori Muto (Takashi Inui 57’)
Australia: Mat Ryan, Ivan Franjic, Alex Wilkinson, Trent Sainsbury, Aziz Behich, Mile Jedinak, Matt McKay (Tim Cahill 73’), Massimo Luongo (Mitch Nichols 63’), Robbie Kruse (Aaron Mooy 88’), Mathew Leckie, James Troisi (Mark Bresciano 63’)
Scorers: Konno 61’, Okazaki 68’, Cahill 90+2’
Venue: Yanmar Stadium, Osaka