Australia's hopes of automatic qualification for the World Cup in Qatar have ended with a whimper while their tactical inadequacies were badly exposed by Japan.

The Japanese sunk the Socceroos 2-0 with a late double from Kaoru Mitoma on Thursday to book their spot at a seventh straight World Cup finals and send Australia to the intercontinental play-offs.

It's a difficult road ahead for Graham Arnold's side, who will now have to beat the third-placed team in Asia's other qualifying group. Should they win that, they then face South America's fifth-best side.

Winning both play-offs appears unlikely, because on Thursday's showing they look badly short in all departments.

At the back, the scrambling of Milos Degenek and goalkeeper Mat Ryan kept them in the contest when Japan countered down the field with speed and purpose.

If Liverpool's Takumi Minamino had been on song, he could well have had a first-half hat-trick.

Australia had no anchor in midfield. Gianni Stensness was cumbersome and Connor Metcalfe looked out of his depth.

It made the decision to keep Denis Genreau, who has been starring in France's Ligue 2 with Toulouse, all the more puzzling.

"I needed more of a defensive-minded No. 6 because Minamino comes inside all the time," Arnold said.

"In my view, we couldn't afford Minamino to be free the whole time because he'd damage us and Denis Genreau plays as a No.10 in France and we decided to play Ajdin Hrustic tonight."

Hrustic was Australia's best in the final third but he wasn't helped by the fact he was shadowing Mitchell Duke up top.

Duke hasn't scored in nine straight games for his club Fagiano Okayama in the Japanese second division and, barring one chance at the end of the first half, never really posed any threat.

The idea was clearly to use his physicality to break down the Japanese but it was akin to opening a tin with an axe, and a blunt one at that.

All the while, Jamie Maclaren was unused until the 85th minute and wasn't going to feature anyway in their final qualifier against Saudi Arabia next week because he is getting married.

When his country needed attacking impetus, Maclaren, who has 12 goals in 18 games for Melbourne City this year, spent most of the second half warming up.

"Jamie's always been a player who can score a goal at anytime in the game," Arnold said.

"I thought that against the Japanese's big centre-backs we needed Mitchell Duke.

"And when he ran out of legs we needed someone who can use their body well like Bruno (Fornaroli) and I thought Bruno did well when he came on."

Perhaps the most revealing response to the Socceroos' qualification woes came when Arnold was asked about his substitutions and how they underlined Australia's standing in Asian football.

This was Japan's first win over the Socceroos in Australia since 1998 and Arnold had brought on Melbourne City's 20-year-old forward Marco Tilio to change the game.

Japan, on the other hand, had deployed 69-cap striker Genki Haraguchi, an experienced campaigner in the Bundesliga.

"If you notice that, you write what you think," hissed Arnold.