The #23 car shared by Tsugio Matsuda and Ronnie Quintarelli will have to serve the penalty during the early stages of the 100-lap race on Sunday, with the exact timing of the announcement at the discretion of race control.
It follows Matsuda's crash at 130R in the previous race at Suzuka in June, which left the works NISMO-run Z destroyed.
Chassis changes during the season are not permitted by the GT500 regulations except in cases of force majeure.
Matsuda's crash was not counted as force majeure as he was deemed responsible for causing the collision with the #30 apr Toyota GR86 GT300 car that triggered the incident exiting 130R, which also claimed the #87 JLOC Lamborghini Huracan GT3.
The two-time GT500 champion was handed three penalty points as a result.
It marks the second time this season a GT500 team has taken a penalty for a chassis change, as the ARTA Honda squad elected to replace its chassis ahead of the opening round of the season at Okayama.
On that occasion, Tomoki Nojiri and Toshiki Oyu recovered to finish third in a race heavily influenced by bad weather.
Saturday morning's opening practice session was led by the #16 ARTA Honda of Nirei Fukuzumi, while Nojiri was second-fastest in the sister #8 machine.
Oyu drove two stints in the car as he tested his fitness to drive following the collarbone injury he sustained last month. Registered third driver Iori Kimura did not appear in practice, but did appear in the subsequent Full Course Yellow test.
The session ended with a red flag after the SARD Toyota of Yuhi Sekiguchi stopped with an apparent mechanical issue during the 10 minutes of GT500-only running.
Elsewhere, it has been announced that gentleman racer Yuki Tanaka will not participate this weekend in the NILZZ Racing Nissan GT-R NISMO GT3 due to illness.
Tanaka's team-mates Taiyou Ida and Takumi Sanada will instead tackle the Fuji race as a duo.
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