Keisuke Honda struck his third 2015 Asian Cup goal to send Japan into the last eight, but the holders have yet to play their best football.
Japan advanced to the quarter-finals of the Asian Cup with a 2-0 win over Jordan on Tuesday, but the reigning champions still appeared to be holding back.
Keisuke Honda gave Japan the lead in the first half, tapping in at the back post after Jordan goalkeeper and captain Amer Shafi could only parry Shinji Okazaki's drive across goal.
It was Honda's third goal of the tournament after a penalty in each of Japan's previous wins - a 4-0 triumph over debutants Palestine and a 1-0 victory against Iraq.
Japan wasted numerous opportunities before adding to Honda's goal in the 82nd minute through Shinji Kagawa.
But although Japan topped Group D with nine points and three clean sheets, the performance in Melbourne was not up to the level that many expect of Javier Aguirre's side in Australia.
The match settled into a predictable rhythm early on with Japan dominating possession, although their ball movement was too slow to truly threaten Jordan for the opening five minutes.
Jordan looked to counter-attack at speed on the rare occasion they did get the ball, but failed to string enough passes together to get into the final third.
In the 10th minute, Jordan were given a clear indication of Japan's threat when Takashi Inui hit the back of the net after a cut-back from Kagawa, but the Borussia Dortmund midfielder was just offside.
Ray Wilkins' Jordan were keen to disrupt Japan's flow and their physical intentions resulted in an early yellow card for Mohammad Mustafa, who raked his studs down Makoto Hasebe's shin.
Mustafa's lunge was not the only poor tackle by Jordan and the Middle Eastern side could do little when Honda opened the scoring in the 24th minute.
Hamza Al Dardour should have done better when his shot was blocked soon after, while Japan went straight up the other end to win two corners in succession.
The second saw Masato Morishige's header force Shafi into a save from just three yards.
Aguirre's men were suddenly flying with Shafi forced to punch a dangerous cross away before Okazaki hit the side netting, but Jordan held on to trail by only one goal at the break.
The loss saw Jordan eliminated with Iraq - 2-0 winners over Palestine - the other team to progress from Group D.
Okazaki could have made it 2-0 immediately after the break, but Shafi smothered the ball at the striker's feet with the Mainz forward surprisingly yellow carded for the clash.
Wilkins had made two substitutions at half-time with Ahmad Hayel and Monther Abu Amara replacing Yousef Al Rawashdeh and Abdallah Deeb, and they seemed to inspire his team.
Hayel, in particular, looked lively as Jordan kepts Japan pinned back for prolonged periods, but Aguirre's side still looked most likely to score with Yasuhito Endo shooting just over the bar, Honda having another goal ruled out for offside and Maya Yoshida heading wide.
Japan finally got their second goal with eight minutes remaining, with Yoshinori Muto teeing up Kagawa, whose side-footed effort was parried into the net by Shafi.