TOM'S driver Miyata came from 12th on the grid to pass Tsuboi around the outside of Turn 1 on the penultimate lap of the 31-lap race to seal his first win in the Japanese single-seater category.
Miyata had vaulted into contention thanks to a safety car period that was prompted when Nojiri and Oyu came to blows on the latter driver's out-lap, putting both in the barriers and out of the race.
Ryo Hirakawa made a late pass on Liam Lawson to finish third, completing an-all Toyota podium.
After an aborted start, owing to Dandelion Racing's Tadasuke Makino failing to get going from the grid, TGM Grand Prix poleman Oyu led the opening stages as Inging's Tsuboi and Nojiri settled into second and third places.
Lawson however was the driver on the move, jumping from eighth on the grid to fourth on the opening lap, and on the third lap he managed to clear Mugen team-mate Nojiri to move up to third.
Nojiri meanwhile appeared to be struggling, dropping another place to Kondo Racing man Kenta Yamashita.
When the pit window opened on lap 10, Lawson was first of the leaders to come in for his mandatory stop, followed by Tsuboi next time around.
Lawson came out behind Tsuboi and was unable to take advantage as the Inging driver got his tyres up to temperature.
Nojiri likewise pitted on lap 11, jumping back ahead of Yamashita in the process, but Oyu decided to delay his stop until lap 19, by which time Miyata had made his way up to second by virtue of staying out.
While Tsuboi and Lawson cleared Oyu with the undercut effect, Nojiri came out right behind the TGM driver and was looking for a way past as they entered the first sector.
But Nojiri misjudged it and rear-ended Oyu, causing both cars to spear into the barriers and putting both out of the race.
The subsequent safety car allowed Miyata and others, including Impul driver Ryo Hirakawa, to complete their pitstops with minimal time loss, but Tsuboi maintained the lead from Lawson, with Miyata slotting into third ahead of Hirakawa.
When the race resumed on lap 24, Lawson was immediately under pressure from Miyata on fresh tyres, with the TOM'S man getting the move done at Turn 1 at the start of the 26th lap to grab second.
Miyata then cruised up to the back of Tsuboi, and while the Inging driver had been saving his Overtake System allocation for the final showdown, he was powerless to resist an inspired Miyata, who got a superior run out of the chicane to set up a bold outside move at Turn 1 on lap 29.
From there, Miyata cruised to his first Super Formula win and a first in nearly two years for TOM'S by three seconds from Tsuboi.
At the same time as the lead battle was decided, Hirakawa passed Lawson for a third with a near-identical move to make it an all-Toyota podium.
Yamashita had to be content with fifth place ahead of Sena Sakaguchi in the second Inging machine and Kazuto Kotaka, who scored his best finish in Super Formula yet with seventh for Kondo.
Giuliano Alesi (TOM'S), rookie Cem Bolukbasi (TGM) and Nirei Fukuzumi (ThreeBond) completed the points scorers.
Besides Nojiri and Oyu, the only other non-finisher was Nakajima Racing's Ren Sato, who suffered a technical problem shortly after the aborted start.
Super Formula - Suzuka race results (30 laps)
| Cla | Driver | Team | Gap | Interval |
|---|---|---|---|---|
| 1 |  Ritomo Miyata |
Vantelin Team TOM'S | ||
| 2 | Sho Tsuboi |
JMS P.mu/cerumo-INGING | 3.022 | 3.022 |
| 3 | Ryo Hirakawa |
ITOCHU ENEX TEAM IMPUL | 3.404 | 0.382 |
| 4 |  Liam Lawson |
Team Mugen | 4.130 | 0.726 |
| 5 | Kenta Yamashita |
Kondo Racing | 8.709 | 4.579 |
| 6 | Sena Sakaguchi |
JMS P.mu/cerumo-INGING | 12.366 | 3.657 |
| 7 | Kazuto Kotaka |
Kondo Racing | 13.071 | 0.705 |
| 8 |  Giuliano Alesi |
Vantelin Team TOM'S | 15.213 | 2.142 |
| 9 |  Cem Bolukbasi |
TGM Grand Prix | 15.728 | 0.515 |
| 10 | Nirei Fukuzumi |
ThreeBond Racing | 16.124 | 0.396 |
| 11 | Naoki Yamamoto |
TCS Nakajima Racing | 16.662 | 0.538 |
| 12 | Nobuharu Matsushita |
B-Max Racing Team | 18.095 | 1.433 |
| 13 | Kazuya Oshima |
docomo business ROOKIE | 18.297 | 0.202 |
| 14 | Kamui Kobayashi |
Team KCMG | 20.130 | 1.833 |
| 15 | Tadasuke Makino |
Dandelion Racing |
20.983 | 0.853 |
| 16 | Yuji Kunimoto |
Team KCMG | 26.393 | 5.410 |
| 17 | Kakunoshin Ota | Dandelion Racing |
26.897 | 0.504 |
| 18 |  Raoul Hyman |
B-Max Racing Team | 34.337 | 7.440 |
| 19 | Yuhi Sekiguchi |
ITOCHU ENEX TEAM IMPUL | 1 Lap | 1 Lap |
| 20 | Toshiki Oyu |
TGM Grand Prix | 11 Laps | 10 Laps |
| 21 | Tomoki Nojiri |
Team Mugen | 11 Laps | 33.449 |
| 22 | Ren Sato |
TCS Nakajima Racing | ||
| View full results | ||||
