Alberto Zaccheroni's side struck three times after the break, with goals from Keisuke Honda, Masato Kudo and Yasuhito Endo wrapping up the win.
The hosts named a strong side which included Shinji Kagawa and Makoto Hasebe, with the Milan-bound Honda starting from the bench.
Zaccheroni had urged his side to work well as a unit in the friendly fixture and he will have been pleased to see his side make much of the early running.
Maya Yoshida had the best of Japan's opening chances, heading a deep corner from the left narrowly over after 19 minutes.
Atsuto Uchida then had a glorious opportunity to put his side ahead after 39 minutes.
However, the Schalke defender blazed over after Christian Alvarez spilled a cross in the area.
Five minutes after the break, Japan had their lead, when Honda, introduced at the break, headed home a Yuto Nagatomo cross from the left.
After 69 minutes, Japan were 2-0 up with through Kudo.
Hasebe split the visitors' defence in two allowing Kagawa to play in Kudo who bundled the ball in from close range.
Endo made it three with 14 minutes to go, curling home a free-kick thanks to a deflection off the Guatemala wall - giving Zaccheroni's men a boost going into their friendly with Ghana on Tuesday.
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