The Tunisians looked set to spoil the Bosnian coach's opening night as they comfortably held a much-changed Japanese side at bay until the hour mark when Keisuke Honda and Shinji Kagawa came on to spark problems in the final third.
The two combined down the left and Honda sent over a deep cross which Shinji Okazaki, another second-half replacement, headed home at the back post in the 78th minute.
The goal brought a rare smile from Halilhodzic in his first game since succeeding Javier Aguirre, who was sacked last month amid fears that Japan's hopes of qualifying for the 2018 World Cup could be hindered by the Mexican's involvement in a match-fixing investigation in Spain.
Honda bagged the second four minutes later after Tunisia goalkeeper Moez Ben Cherifia could only parry a Kagawa cross from the left into the path of the AC Milan attacker.
Halilhodzic, who stood stony-faced for most of the game, had named an experimental lineup with only Tuesday's fixture against Uzbekistan in Tokyo to come before Japan begin their bid to qualify for the World Cup.
One of the debutants, Takashi Usami, almost scored a third but the Gamba Osaka forward's effort was just tipped against the post.
(Writing by Patrick Johnston in Singapore, editing by Ed Osmond)
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