The #9 Mercedes-AMG GT3 Evo shared by Ryohei Sakaguchi and Liang Jiatong was involved in an incident with the #88 JLOC Lamborghini Huracan GT3 Evo late in the rain-soaked Okayama race, bringing out the safety car.
Chinese driver Jiatong had been battling JLOC rival Takashi Kogure for sixth place at the time of the incident, which effectively spelled the end of the race as worsening weather conditions resulted in the red flags being shown thereafter.
On Tuesday, Pacific posted a brief statement on its Twitter account saying that the damage incurred in the crash will prevent the team from participating in the Fuji 450km on May 3-4.
It reduces the GT300 class to 26 cars and the full field size to 41 cars for the traditional Golden Week race.
The statement read: "Since the Okayama race, the team has been working as a whole to restore and recover the car, but we came to this decision after discussing with the drivers and other stakeholders.
"We will now aim to make a full recovery from Round 3 [at Suzuka on June 3-4], so we ask for your continued support and encouragement."
Sakaguchi and Jiatong were due to be joined by Pacific's designated third driver Shintaro Kawabata for the Fuji race.
