Three-time series champion Yamamoto followed up his pole position in the morning's qualifying session with a lights-to-flag victory in wet conditions, his first in the series in two years.
Since switching from Dandelion Racing to Nakajima at the start of last year, sixth place at Fuji in 2021 had been Yamamoto's best finish prior to Saturday as he struggled to recapture his past form.
Helped by a safety car start reducing the risk of being passed for the lead, Yamamoto admitted that the one and only caution period of the race came at the right time for him, as nearest pursuer Sacha Fenestraz had been catching just prior, as well as the arrival of more rain mid-race.
"As it rained right before the start, I don't think any team had a perfect wet set-up and nobody in particular had an advantage, so I felt it would all come down to the driver's efforts," said Yamamoto.
"I was saving [my tyres] so that I was ready to push at any moment, but to be honest, when the cars behind started catching me, at that point I didn't have anything in reserve.
"In the middle of the race the track dried somewhat and my tyre pressures increased, so I was hoping for more rain or a safety car, and then both of these things happened. It felt like, 'this is how things should be when you win'.
"Up to this point things were not going well, and we weren't doing anything different from before, so when we won the fact that everything went so smoothly is strange. But I'm glad that we never gave up or got discouraged."
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Yamamoto's victory was the first for Nakajima Racing since the 2020 season, and also marked his race engineer Yuki Katoh's first victory since his one and only triumph working with Alex Palou in 2019.
Speaking to Motorsport.com's Japanese edition post-race, Katoh said he could not feel relieved about his driver's success owing to the special circumstances in which it was achieved.
"In the race the weather was a big help," he conceded. "In Q2, there was a lot of traffic behind us, which we were careful to avoid, but on a level playing field I'm not sure how it would have gone.
"Therefore I can't feel relieved... it feels like we are only halfway there [on the road to recovery]. That said, it was Naoki's experience and skill that led to this victory, so I am grateful for that."
