Takuma Asano gave the Japanese the lead four minutes before the half-time break when he was left unmarked to slide Yuto Nagatomo's cross beyond Mat Ryan to put Japan in front after Mathew Leckie had earlier hit the post for the Socceroos.
Eight minutes from time Yosuke Ideguchi put the result beyond doubt with a thunderous strike from outside the area that sent the sold out Saitama Stadium into a frenzy.
Victory moves Halilhodzic's side onto 20 points from nine games. With Saudi Arabia losing to the United Arab Emirates on Tuesday evening, the Japanese are now guaranteed first place in the group no matter what happens in the final round of matches next week.
Australia's hopes are now out of their own hands. Ange Postecoglou and his team need to beat Thailand in Melbourne on Tuesday, and hope Japan avoid defeat when they travel to face second-placed Saudi Arabia.
The Japanese, who have joined Iran in qualifying for next year's finals, were the only team to confirm their place in Russia on Thursday during another tense evening's action across Asia.
South Korea were unable to pick up the win they needed against Iran at Seoul World Cup Stadium to seal their place at an eighth straight finals, despite Saeid Ezatolahi's sending off seven minutes into the second half.
Playing their first competitive match since Shin Tae-Yong took over as head coach, following the sacking of Uli Stielike in June, the Koreans picked up a solitary point that leaves them in second place in Group A.
The Taeguk Warriors will take on Uzbekistan on Tuesday knowing a win in Tashkent will see them book their place in Russia. The Uzbeks will have to pick themselves up after a late 1-0 loss to China that keeps Marcello Lippi's team in with a slim chance of qualifying.
Gao Lin scored the only goal of the game from the penalty spot six minutes from time after Feng Xiaoting was adjudged to have been fouled in the area, with the win meaning Lippi's team can still qualify for the playoffs.
China will have to defeat Qatar by a big margin and hope other results go their way, with the Qataris now eliminated following their 3-1 loss at the hands of Syria.
Omar Khrbin scored twice to give the Syrians a win that moves them into third place in the group, leapfrogging the Uzbeks on goal-difference to go within one game of qualifying for their first-ever World Cup finals.
Syria, who have been forced to play all of their home games in neutral venues due to the security situation at home, take on Iran in Tehran on Tuesday knowing a win over Carlos Queiroz's side could be enough to earn a place in December's World Cup finals draw.
In the other game taking place on Thursday evening, a penalty five minutes from time by Saad Abdulameer earned Iraq a 2-1 win over Thailand. Both teams had already been eliminated before the game.
