Despite winning their first two games, Japan still needed a point at the Rectangular Stadium to win the group and set up a quarter-final against United Arab Emirates in Sydney on Friday.
Striker Keisuke Honda gave them the halftime lead with his third goal in three games at the tournament and Shinji Kagawa added the second eight minutes from time.
Jordan needed an upset victory to have any realistic chance of progressing but were starved of possession before the break and ran out of steam after a strong start to the second half.
Japan's neat interplay in the final third was almost irresistible and the four-times champions, who fielded the same starting side for the third straight match, will go into the knockout stages with plenty of confidence.
The opening goal came in the 24th minute when Takashi Inui's neat pass set the lively Shinji Okazaki free in the box and when Jordan goalkeeper Amer Shafi parried the striker's shot, Honda was on hand to tap the ball into the net from the angle.
It was a first goal from open play after two penalties for Honda, who hit the woodwork three times in Japan's last match against Iraq.
Jordan coach Ray Wilkins made changes at halftime and it was one of the substitutes, winger Munther Abu Amarah, who got their first shot on goal in the 57th minute.
Japan goalkeeper Eiji Kawashima dealt with the threat at his near post and within a minute Honda had the ball in the back of the net only to be called back by a marginal offside call.
Shafi continued to impress in the Jordan goal but he was unable to prevent Japan going 2-0 up in the 82nd minute.
Yuki Muto, who had just come on as a substitute for Okazaki, was set free into acres of space down the left wing and had plenty of time to pick out Kagawa, who side-footed the ball into the net from six metres out.
Honda still had time to renew his acquaintance with the woodwork when he lashed a shot across Shafi only for the ball to come off the far post in stoppage time.
(Reporting by Nick Mulvenney, editing by Amlan Chakraborty)
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