Ronnie Quintarelli and Tsugio Matsuda had finished second aboard the #23 NISMO Nissan Z in the 450km race, marking their first visit to the podium since the Okayama curtain-raiser.
However, they were excluded following post-race technical inspection due to an infraction relating to their car's skid block.
It means the SARD Toyota GR Supra of Yuhi Sekiguchi and Yuichi Nakayama moves up to second behind the winning ARTA Honda NSX-GT shared by Nirei Fukuzumi and Hiroki Otsu.
Inheriting the final place on the podium is the Rookie Racing Toyota of Kenta Yamashita and Kazuya Oshima.
The disqualification comes as a major blow to Quintarelli and Matsuda's title ambitions, as they had closed to within nine points of NDDP Nissan pair Katsumasa Chiyo and Mitsunori Takaboshi.
Instead, they now trail their points-leading Nissan colleagues by 24 points with three races remaining.
Chiyo and Takaboshi's points lead has been cut to four points as a result of TOM'S Toyota duo Sho Tsuboi and Ritomo Miyata picking up a single point after being promoted to 10th in the final results.
Fukuzumi and Otsu are 12 points away from the lead following their victory on Sunday.
