The #16 ARTA car of Fukuzumi and Otsu took advantage of a well-timed first pitstop under full-course yellow to cement their early lead, ultimately beating NISMO pair Tsugio Matsuda and Ronnie Quintarelli to victory by just over 10 seconds.
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.
Otsu took the start from pole position and maintained a two-second lead over Quintarelli’s NISMO Nissan in the early laps until the first full-course yellow was thrown at the end of lap 11 of 77 when the Team LeMans Audi shed its left-rear wheel and stopped on track.
ARTA reacted quickly and brought Otsu into the pits before the FCY was called, but Nissan squad Kondo Racing was less fortunate, with Kohei Hirate being handed a 60-second stop-and-go penalty for being judged to pit under FCY.
Quintarelli took over the lead and stayed out until lap 18, but such was the advantage of pitting under FCY that Otsu emerged with a 42-second advantage once the dust settled on the first round of stops.
During the second stint Quintarelli began to close the gap, and had the deficit down to 26 seconds before coming in for his second stop and handing over to Matsuda on lap 42.
Two laps later, Otsu pitted from the lead to make way for Fukuzumi, whose lead was down to 15 seconds by the time the second pitstop cycle was completed.
Matsuda continued to chip away at the lead in the closing stint, but Fukuzumi was able to stabilise the gap, going on to score his fourth GT500 win and a first for Otsu in what will be the NSX-GT's final visit to Suzuka before it is replaced by the new Civic Type R-GT next year.
An entertaining battle for third between two Toyota crews was resolved in favour of SARD, as Nakayama managed to keep Kenta Yamashita’s Rookie Racing GR Supra at bay.
Sekiguchi had started the SARD car down in 11th, but an early first stop on lap 15 allowed him to jump up the order. He passed the championship-leading #3 NDDP Nissan, which had stopped even earlier, for third before handing over to Nakayama on lap 43.
Rookie went for an unconventional strategy of driver changes at both pitstops, as Yamashita did both the first and final stints, but fell just short of overhauling Nakayama late on.
Real Racing Honda pair Koudai Tsukakoshi and Nobuharu Matsushita finished fifth ahead of the Impul Nissan of Kazuki Hiramine and Bertrand Baguette after Hiramine made a late pass on the Cerumo Toyota of Hiroaki Ishiura.
NDDP Nissan duo Katsumasa Chiyo and Mitsunori Takaboshi ended up out of the points in 13th place, with the team’s decision to pit as early as lap six backfiring.
But the pair keep the lead of the championship as their nearest rivals, TOM’S Toyota drivers Sho Tsuboi and Ritomo Miyata, likewise failed to score in 11th place. Fukuzumi and Otsu meanwhile jump up to third place, 12 points off the lead.
ARTA’s #8 car shared by Tomoki Nojiri and Toshiki Oyu suffered a nightmare race that culminated in Oyu picking up front-right damage while batting the other TOM’S GR Supra of Giuliano Alesi at the hairpin.
Oyu triggered a third full-course yellow period by going into the gravel at 130R, and although he managed to coax his NSX-GT back to the pits - but he was awarded a 60-second stop-and-go for stopping under the very caution that he had triggered.
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.
