Aguirre was missing from the sidelines as he returned to his native Mexico to attend a ceremony, with Stuart Gelling taking charge in his absence.
The hosts essentially ended the friendly fixture by half-time as goals from Maya Yoshida, Keisuke Honda and Yasuhito Endo helped gave them a 3-0 lead at the break.
There was no let-up for Honduras in the second half as a double from Takashi Inui sandwiched a strike from fellow substitute Yohei Toyoda.
Yoshida opened the scoring in the ninth minute when he nodded home at the back post after Honduras goalkeeper Donis Escober did well to save Shinji Okazaki's original header.
Honda then got in on the action five minutes before the break with a simple finish in the area, before Endo made it 3-0 with a rasping 25-yard drive a minute before half-time.
Inui got in on the act three minutes after the break with a calm side-footed strike at the back post after making a late run from the left, before Toyoda swept home the fifth after a swift counter-attack.
Inui completed the rout with a drilled shot from eight yards, as Japan continued their warm-up for next year's Asian Cup in emphatic fashion.
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