The #36 Toyota GR Supra shared by Sho Tsuboi and Ritomo Miyata was on course for at least second place until their charge was ended by a loose front left-wheel in the closing stages of what proved to be a weather-shortened curtain-raiser.
Miyata, who took over from Tsuboi as the track dried out following an earlier shower, led a queue of cars into the pits under caution to change back to wet tyres after another deluge hit the former Pacific Grand Prix venue.
But amid chaotic scenes in a crowded pitlane, the #36 car's air jack was released too early, prompting Miyata to leave the pit box before the front-left wheel had been fully tightened. Moments later, Miyata inevitably crawled to a halt on track as the offending wheel came loose.
The sister #37 car of Ukyo Sasahara and Giuliano Alesi had already been ruled out of contention for a top result by a one-minute stop-and-go penalty, awarded when Sasahara entered a closed pit under an early full-course yellow period amid the first rain shower.
They eventually finished a lapped 13th behind another car that was hit by the same punishment, the Team Kunimitsu Honda.
TOM'S team director Jun Yamada said the double disaster would prompt his team to do some serious soul-searching prior to the next race at Fuji in two weeks.
"We have to go away and deeply reflect on this," Yamada told Motorsport.com. "Car #37 went a lap down due to a penalty, so I was really hoping we could get a strong result with car #36, and we were running in a good position.
"We staggered the timing of the pits [with the two cars], but… what happened was unbelievable. It was just a simple human error."
Although the race did not get going again after the pitlane disaster that put the #36 car out, Yamada believes that had the race resumed, Miyata would have been in a position to challenge Tsugio Matsuda's Nissan for the win.
"I think there would have been a good fight with car #23 [Matsuda], but in the heavier rain I think we had an advantage," said Yamada. "I think we could have gone for the win, so it’s a shame. It just wasn’t our day!"
Looking back on the penalty given to the #37 TOM'S crew, Yamada admitted that the team simply took a risk in the worsening conditions that ultimately didn't pay off when it emerged the FCY had been called.
"The timing was right on the edge and I wasn’t sure if there would be a penalty," said Yamada. "But the driver [Sasahara] said he couldn’t see [the FCY display in the cockpit] either.
"It was just a mistake in terms of timing, but it was a strategy that we adopted knowing that it would be on the edge, so it’s just one of those things."
For his part, Sasahara said post-race that such was the rainfall at the time that he felt he had no choice but to pit despite the risk of a penalty.
"The rain suddenly started coming down hard, so we were in the same position as the #100 [Kunimitsu Honda]," he told Motorsport.com. "We had to pit then, and as a team we all agreed about going into the box.
"So it was just bad luck, bad timing. If the FCY came out just a couple of seconds later, it would have been the perfect strategy."
However, Sasahara added that the penalty didn't detract from his personal satisfaction about the potential he displayed on his Toyota SUPER GT debut.
"It felt like the car’s performance was there," said Sasahara. "The #36 was pretty quick, but we had a good chance to be on the podium.
"Of course the result is a shame, but for my first race in Toyota, the performance was pretty much a match for the best Toyota. So now I am really looking forward to the next race. I think I showed what I can do."
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