The Asian champions, 3-0 winners over Oman on Sunday, travel to Brisbane next to take on fierce rivals Australia on Tuesday and will be in a confident mood after back-to-back blowouts in Saitama.
Ryoichi Maeda put Japan ahead with a looping header in the 18th minute, before Honda quickly doubled the home side's lead, finishing in style after a clever ball from Yasuhito Endo.
Jordan forward Abdallah Deeb was then sent off after receiving his second yellow inside two minutes for leaving Japan captain Makoto Hasebe with a cut head from a stray elbow.
Japan took advantage, Honda tapping in his second on the half hour and Shinji Kagawa squeezing in a fourth in the 35th minute after more horror defending from Jordan.
Honda, who also found the net against Oman, completed his hat-trick in the 53rd minute from the penalty spot before being replaced to conserve his energy for the Socceroos.
Substitute Yuzo Kurihara headed Japan's sixth a minute before time to further boost their goal difference and hand Jordan a record-equalising loss.
Jordan drew their opening Group B game 1-1 with Iraq, currently under the stewardship of former Japan coach Zico.
Oman host Australia later on Friday.
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