Honda – who has struggled for form at club level with Milan – was integral in both goals for the hosts in Oita, creating the first for Shinji Okazaki, before finding the net himself with eight minutes to play.
Mainz striker Okazaki needed six minutes to break the deadlock after coming on midway through the second half, the 28-year-old heading home Honda's deep cross much to the relief of his new coach.
Victory was assured when an unmarked Honda slid home Kagawa's cross four minutes later, enabling the healing process to begin after Japan's early exit at the Asian Cup two months ago.
Halilhodzic – who replaced Javier Aguirre earlier this month – saw his side dominate possession throughout their friendly, but in the first half they lacked a finishing touch.
Kengo Kawamata went closest with a header that struck the crossbar after 21 minutes, while Makoto Hasebe and Yoshinori Muto both wasted good openings with weak efforts.
The introduction of Kagawa and Honda was the catalyst for their change in fortunes, the pair entering the fray 13 minutes after the break.
Honda was immediately involved as his corner was converted by Maya Yoshida only for the referee to disallow the goal for a foul in the penalty area.
The Milan playmaker's creativity soon fashioned another chance, though, as he and Kagawa combined before Okazaki rose at the back post to finally beat Moez Ben Cherifia.
With the deadlock broken, Japan immediately grew in confidence and Honda secured the win, the sub converting after Tunisia failed to deal with Kagawa's right-wing cross.
Takashi Usmai could have added a third in stoppage time, but the forward was denied a debut goal by the post, however it mattered little as Japan made a positive start to a new era.
