Milligan, who took the captain’s armband in the place of Mile Jedinak, was visibly shattered after the game, struggling to comprehend exactly how Australia's bright start ended in them being outplayed and outscored in front of almost 60,000 Japanese fans.
Now the Socceroos’ fate rests on how they perform against Thailand on Tuesday in Melbourne and how Saudi Arabia fare against Japan.
Both Australia and the Saudis are level on points, but the west Asian nation has a superior goal difference of two, which could prove decisive.
“We set up and prepare for these matches, so to play the way we did was pretty disappointing. We have to re-group and do so quickly,” Milligan said.
“We can't ignore what's happened but we need to move on with it. Obviously we learn, whether we win or lose, so that we can become better.
“We're here for a day before we travel home so we'll look at it again, we'll look where we were good, where we fell short and we'll make sure we put in a more complete performance.”
Although the Socceroos were right in the contest in the opening half-hour, Milligan said he noticed that Japan played a strategically clever game, one that denied the Socceroos space where they needed it.
“Early on they picked and chose when to press us. They crowded that midfield area and I don't think we moved the ball quite quick enough to shift them about,” he said.
“They were still comfortable. I don't think we found answers quick enough. Then the first goal they scored a was a cheap one. It was a knife to the heart.”
When it was put to Milligan that the absence of Aaron Mooy – absent with a virus – was the reason Australia was soundly beaten in midfield, the skipper disagreed, saying there were no excuses.
“No, not at all, because we have 23 players here. We are all ready to play, there are many midfielders in the camp and for the last four years we have been very vocal about the whole squad,” he said.
“It's not one player. Obviously it's disappointing to lose players but we didn't have Tommy [Juric] available all week with a slight injury. But there's many players that can step in and have done a job before. I don't think that's a factor at all.”
With Japan already qualified, there’s only one direct qualification spot left for the Socceroos and Saudi Arabia to fight for, with the third-placed team entering into the elongated play-off route – a fate the Socceroos are desperate to avoid.
According to Milligan, a much-improved performance against Thailand will happen if the team executes the basics correctly.
“I think we just need to get back to what we're good at. We're good at moving the ball quickly, we're good at moving the opposition around and we're good at picking times to penetrate and getting balls into the box,” he said.
“That's what we need to get back to and if a team wants to sit off us a little bit, we need to find answers in other areas. I have no doubt we will regroup and put in a wonderful performance on Tuesday night and we'll be fine.”
