Nakajima Racing driver Yamamoto executed the 37-lap race to perfection after the rain arrived just minutes prior to the start, keeping Fenestraz at bay throughout and surviving a late safety car restart en route to the ninth win of his career and his first at his local track.
As well as ending a two-year winless run for Yamamoto, it also marks Satoru Nakajima's eponymous team's first victory in two years.
The rain ahead of the start led to a safety car start as the entire field scrambled to change their slick tyres to wets on the grid, with the first three laps taking place under caution before the race began in earnest on lap 4.
Yamamoto led comfortably from Fenestraz, Toshiki Oyu and points leader Tomoki Nojiri amid the increasing spray, with the gap between the lead two cars growing to five seconds by the end of lap 12.
The order at the front remained static until Oyu in the second Nakajima car slowed and dropped to ninth on lap 14, suffering gearbox issues that would eventually prompt Oyu to bring his car back to the garage.
Fenestraz began to eat away at Yamamoto's lead in the middle phase of the race, closing to within two seconds before the safety car was deployed on lap 27 when Ryo Hirakawa got his Impul machine beached in the gravel near the pit entrance.
At the restart on lap 31, Yamamoto fended off an early attack from Fenestraz and the three-time champion eventually took the chequered flag by 5.337s, with Nojiri following Fenestraz home in third.
With Hirakawa failing to score, Kondo Racing's Fenestraz takes over as Nojiri's nearest rival in the championship, sitting 30 points behind the Mugen driver with three races remaining.
Tadasuke Makino (Dandelion) finished fourth after holding off Sho Tsuboi (Inging) for the entire race, while Kenta Yamashita (Kondo) likewise had a relatively uneventful run to sixth place.
Ukyo Sasahara (Mugen) was one of the biggest movers after the safety car restart, managing to pass Ritomo Miyata (TOM'S) for seventh place on the final lap to move up five places from his grid slot.
Completing the points were the surviving Impul car of Yuhi Sekiguchi and Hiroki Otsu in the second Dandelion car.
Giuliano Alesi (TOM'S) was one of a handful of cars to pit for fresh wet tyres under the safety car, and this strategy appeared to pay dividends as he climbed into the points, at one point passing Sekiguchi for ninth.
However, the Frenchman spun soon after, dropping him down the order, with his chances of scoring points also compromised by a five-second penalty for running off-track during the safety car period.
He took the chequered flag in 12th, one place behind Nobuharu Matsushita (B-Max), but the penalty dropped him behind Red Bull junior Ren Sato in 13th.
Motegi Super Formula - Race results:
| Cla | # | Driver | Team | Laps | Gap |
|---|---|---|---|---|---|
| 1 | 64 |  Naoki Yamamoto |
TCS Nakajima Racing | 37 | |
| 2 | 4 |  Sacha Fenestraz |
Kondo Racing | 37 | 5.337 |
| 3 | 1 | Tomoki Nojiri |
Team Mugen | 37 | 7.210 |
| 4 | 5 | Tadasuke Makino |
Dandelion Racing |
37 | 12.628 |
| 5 | 38 | Sho Tsuboi |
P.MU/CERUMO?INGING | 37 | 13.575 |
| 6 | 3 | Kenta Yamashita |
Kondo Racing | 37 | 16.112 |
| 7 | 15 | Ukyo Sasahara |
Team Mugen | 37 | 17.622 |
| 8 | 37 | Ritomo Miyata |
Kuo VANTELIN TEAM TOMS | 37 | 19.323 |
| 9 | 19 | Yuhi Sekiguchi |
Team Impul | 37 | 29.138 |
| 10 | 6 | Hiroki Otsu |
Dandelion Racing |
37 | 29.911 |
| 11 | 50 | Nobuharu Matsushita |
B-Max Racing Team | 37 | 31.493 |
| 12 | 36 | Giuliano Alesi |
Kuo VANTELIN TEAM TOMS | 37 | 33.624 |
| 13 | 53 | Ren Sato |
Team Goh | 37 | 35.948 |
| 14 | 7 | Kamui Kobayashi |
KCMG | 37 | 38.898 |
| 15 | 18 | Yuji Kunimoto |
KCMG | 37 | 41.697 |
| 16 | 14 | Kazuya Oshima |
docomo business ROOKIE | 37 | 42.375 |
| 17 | 39 | Sena Sakaguchi |
P.MU/CERUMO?INGING | 37 | 43.917 |
| 18 | 12 | Nirei Fukuzumi |
ThreeBond Drago CORSE | 29 | 8 Laps |
| 19 | 55 | Atsushi Miyake |
Team Goh | 29 | 8 Laps |
| 20 | 65 | Toshiki Oyu |
TCS Nakajima Racing | 29 | 8 Laps |
| 21 | 20 | Ryo Hirakawa |
Team Impul | 26 | 11 Laps |
| View full results | |||||
