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.
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.
