Goals from Yasuyuki Konno and Shinji Okazaki within seven second-half minutes of each other put the hosts in control of a game in which the visitors had impressed in a goalless opening period.
Australia's record goalscorer Tim Cahill came off the bench to net a looping header - his 36th international strike - though it came too little too late.
Ange Postecoglou's men end the calendar year having won just once and will head into their Asian Cup opener against Kuwait in January off the back of eight defeats in their last 11 fixtures.
Javier Aguirre, on the other hand, will be delighted with the performances of some of his star-name talents as they begin preparations for defending their title on Australian soil.
Postecoglou opted for a youthful and pacy front three of Robbie Kruse, Mathew Leckie and James Troisi with the latter two going close in a fast-paced opening 10 minutes.
Leckie was again in the action with 17 minutes on the clock, meeting Massimo Luongo's cross with a firm header but home goalkeeper Eiji Kawashima was equal to it.
Japan's best chance of the half came five minutes from the break, Shinji Kagawa getting to the byline and cutting the ball back, with Socceroo skipper Mile Jedinak fortunate to see the ball ricochet off his shin and just past a helpless Mat Ryan's left-hand post.
Untroubled for much of the first half, Ryan had to pull off two smart saves to deny both Kagawa and Okazaki within a couple of minutes of the restart.
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 men, but one they did not heed as Konno was left unmarked at the back post from a corner, heading high into the net for just his second international goal.
The experienced defender's only previous strike for his country also came against Australia in a 2012 World Cup qualifier.
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 in the second minute of stoppage time to halve the deficit but the home side held on for a well-deserved victory
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