Katsumasa Chiyo and Mitsunori Takaboshi took full advantage of the mixed conditions in Sunday's 100-lap race in their Michelin-shod #3 Nissan Z, taking their first victory of the season by a commanding 43.9 seconds.
Two Honda NSX-GTs completed the podium, as ARTA duo Hiroki Otsu and Nirei Fukuzumi were best of the Bridgestone runners in second, followed by Team Kunimitsu pair Naoki Yamamoto and Tadasuke Makino in third.
The race was red-flagged after 68 of 100 laps when the Tsuchiya Engineering Toyota GR Supra GT300 car of Seita Nonaka stopped at the side of the track at Turn 3 and started going up in flames.
Such was the severity of the blaze that an initial safety car period gave way to red flags when it became clear that the marshals wouldn't be able to contain the fire immediately. Nonaka escaped uninjured.
The race resumed after an interlude of 50 minutes, in which time a rain shower doused the track, delaying the restart, but the full 100-lap distance was completed before the time limit was reached.
Rain prior to the start meant that the race started behind the safety car for two laps before the green flag was shown on lap three, with all 15 GT500 cars starting the race on wet tyres.
The pole-sitting Kondo Racing Nissan of Daiki Sasaki led initially, but the NDDP car that started fourth in the hands of Chiyo was soon on the move, picking off the ARTA Hondas of Toshiki Oyu and Nirei Fukuzumi to move up to second.
On lap four, Chiyo passed Sasaki to take the lead, but the order would soon be reshuffled as the track dried and the GT500 runners came into the pits to complete their first refuelling stops and change to slick tyres, starting on lap 11.
Chiyo was one of the last cars to come in on lap 15, in the process dropping behind Fukuzumi's ARTA Honda and two cars that opted to short fill to gain track position, the Rookie Racing and SARD Toyota GR Supras.
The Rookie Racing car of Kazuya Oshima had the pace at this stage, passing Fukuzumi to lead on lap 24, and that was how the order remained at the front until the safety car was called on lap 36 when the Max Racing Toyota GR Supra pulled off course on fire.
The race restarted on lap 41 with Oshima leading Fukuzumi, who was then passed by Yuhi Sekiguchi in the SARD car for second.
But Oshima pitted on lap 46 to hand over to Kenta Yamashita, with Sekiguchi coming in one lap later to make way for Yuichi Nakayama, with both cars now effectively locked into three-stop strategies.
Fukuzumi retook the lead as a result ahead of Chiyo, but the car on the move during this phase of the race was the #37 TOM'S Toyota of Ukyo Sasahara, who had made his way up from 12th on the grid to run third.
Chiyo was next of the leaders to stop on lap 56, handing over the NDDP Nissan to Takaboshi, followed by Fukuzumi next time by, with Hiroki Otsu taking over the ARTA machine. But both were vaulted by the TOM'S machine that Giuliano Alesi took over when Sasahara stopped on lap 59.
When the second pitstop phase was complete, Yamashita led Nakayama, but with both cars needing to stop one more time, with Alesi third ahead of Takaboshi and Otsu. That was how the order was when the race was red-flagged for the Tsuchiya Supra's fire.
With more rain arriving just before the planned restart at 1610 local time, the restart was delayed to allow the entire field to switch back to wet tyres. At 1630 the race resumed behind the safety car, and the green flags were shown on lap 72.
In ideal conditions for the Michelin wet tyre, Takaboshi made short work of the three Bridgestone-shod Toyotas ahead of him, passing Alesi, Nakayama and Yamashita in quick succession to lead on lap 75.
By lap 80, Takaboshi had put 12 seconds between himself and the field, virtually doubling his advantage in the next three laps, and finally ending up over 40 seconds clear when the chequered flag fell.
Meanwhile, Otsu surged through from fifth at the restart to run second, and was able to escape the chasing pack as Yamashita and Nakayama made their final stops and Alesi started dropping down the order.
The other ARTA Honda of Tomoki Nojiri, who took over from Oyu at the second round of stops, lost a strong chance of a podium with a spin exiting the final turn, shortly after which Nojiri pitted for slicks as the track dried.
That paved the way for Yamamoto to grab the final spot on the podium as he surged up the order in the closing stages, coming out on top in a late battle with the Dunlop-shod Nakajima Honda of GT500 rookie Kakunoshin Ota.
But both the second and third place Honda NSX-GT crews were hit by post-race penalties, the #16 ARTA entry of Fukuzumi/Otsu and #100 Kunimitsu of Yamamoto/Makino having 40 seconds added to their race times for illegally refuelling and changing tyres at the same time.
Fukuzumi and Otsu drop from second to third as a result, while Yamamoto and Makino slip to sixth position in the revised results.
Nakajima Racing's Honda therefore moved up to second place, with Ota and Takuya Izawa delivering its first podium finish for almost three years.
TOM'S Toyota pair Sho Tsuboi and Ritomo Miyata, who had led the standings heading into the Fuji race, move up from fifth to fourth at the expense of the Kunimitsu Honda.
The Kondo Nissan that started on pole finally finished 10th.
Victory in a topsy-turvy GT300 contest went the way of the #11 Gainer Nissan GT-R NISMO GT3 driven by Keishi Ishikawa and Ryuichiro Tomita.
