Despite running on completely opposing strategies in the 37-lap race, Sekiguchi and Hirakawa ended up first and second respectively in the final few laps and proceeded to battle hard for the victory.
With absolutely no sign of Impul employing team orders despite Hirakawa still being in contention for the title, the Toyota FIA World Endurance Championship star was unable to make use of his fresh tyres and had to settle behind Sekiguchi.
It marked a first win for Sekiguchi since the 2019 Autopolis race and a first one-two for Impul since 2008.
Tadasuke Makino took the final spot on the podium in third, while Tomoki Nojiri closed in on a second successive title with fourth place.
Story of the race
Poleman Toshiki Oyu led at the start as Nojiri managed to jump ahead of title rival Sacha Fenestraz into second, with Fenestraz only just holding off Kondo Racing teammate Kenta Yamashita to maintain third.
Further back, Hirakawa and Sekiguchi were engaged in their own private battle for fifth place, with Hirakawa getting ahead on lap 2.
The order remained unchanged until the pit window opened on lap 10, but surprisingly none of the frontrunners opted to come in for a tyre change, with the first major change of position coming when Yamashita pitted out of fourth place to come into the garage with a technical fault.
That promoted Hirakawa to fourth place, but Sekiguchi had already pitted out of sixth on lap 10, and with several other drivers further down the order also pitting in, Sekiguchi found himself with a large pocket of clean air in which to maximise the advantage of fresh tyres.
As a result, Sekiguchi rapidly closed within range of being able to undercut the leaders, and sure enough when Nojiri became the first of the top group to pit on lap 15, he resumed behind the Impul driver as well as Makino, who had pitted on lap 11.
The next lap, Nakajima Racing man Oyu and Fenestraz pitted together, their positions remaining unchanged despite a slow stop for the former, but both were undercut by Sekiguchi, Makino and Nojiri.
Hirakawa assumed the lead at this stage as Impul split their strategies, leaving the title contender and two-time Motegi winner out until lap 30.
Resuming behind Nojiri in fourth place, the fresh tyre advantage soon became apparent and on lap 32 the Toyota man went all the way around the outside of the points leader at the Turn 11 left-hander.
Two laps later, Makino was defenceless when Hirakawa came up the inside at Turn 5, with attention now turning to how the battle between Impul duo Sekiguchi and Hirakawa would play out.
Hirakawa appeared strongest on the run down to Turn 11, and came close to making a move on the last lap, but Sekiguchi held firm and forced his teammate to the outside and on to the kerbs, Hirakawa's front wheels briefly catching air.
Just 0.943s split the pair as they came across the line, with Makino following 2.4s back in third.
Mugen driver Nojiri was fourth ahead of Oyu and Fenestraz, who conceded three points to the championship leader and will head to the Suzuka finale 32 points in arrears with only 46 left on the table.
Hirakawa remains third overall, 35 points behind Nojiri and still in theoretical contention.
Red Bull junior Ren Sato (Team Goh) made a late-stopping strategy work to his favour to take a solid seventh, as did Ukyo Sasahara, who charged from the back of the grid to finish eighth for Mugen.
Inging pair Sena Sakaguchi and Sho Tsuboi completed the points in ninth and 10th places.
Saturday race winner Naoki Yamamoto finished down in 16th after picking up a five-second penalty for contact with Kazuya Oshima.
Giuliano Alesi almost didn't start the race due to technical issues with his TOM'S machine, but had made strong progress up the field when he had to pit and retire 11 laps from home.
Motegi Super Formula - Race results:
| Cla | # | Driver | Team | Gap |
|---|---|---|---|---|
| 1 | 19 |  Yuhi Sekiguchi |
Team Impul | |
| 2 | 20 | Ryo Hirakawa |
Team Impul | 0.943 |
| 3 | 5 | Tadasuke Makino |
Dandelion Racing |
2.450 |
| 4 | 1 | Tomoki Nojiri |
Team Mugen | 4.713 |
| 5 | 65 | Toshiki Oyu |
TCS Nakajima Racing | 5.985 |
| 6 | 4 |  Sacha Fenestraz |
Kondo Racing | 7.222 |
| 7 | 53 | Ren Sato |
Team Goh | 8.096 |
| 8 | 15 | Ukyo Sasahara |
Team Mugen | 14.316 |
| 9 | 39 | Sena Sakaguchi |
P.MU/CERUMO?INGING | 25.715 |
| 10 | 38 | Sho Tsuboi |
P.MU/CERUMO?INGING | 26.211 |
| 11 | 64 | Naoki Yamamoto |
TCS Nakajima Racing | 39.358 |
| 12 | 50 | Nobuharu Matsushita |
B-Max Racing Team | 40.470 |
| 13 | 18 | Yuji Kunimoto |
KCMG | 42.326 |
| 14 | 6 | Hiroki Otsu |
Dandelion Racing |
42.877 |
| 15 | 37 | Ritomo Miyata |
Kuo VANTELIN TEAM TOMS | 43.165 |
| 16 | 55 | Atsushi Miyake |
Team Goh | 43.799 |
| 17 | 7 | Kamui Kobayashi |
KCMG | 1'09.145 |
| 18 | 14 | Kazuya Oshima |
docomo business ROOKIE | 1'23.217 |
| 19 | 3 | Kenta Yamashita |
Kondo Racing | 8 Laps |
| 20 | 36 | Giuliano Alesi |
Kuo VANTELIN TEAM TOMS | 11 Laps |
| 21 | 12 | Nirei Fukuzumi |
ThreeBond Drago CORSE | 34 Laps |
| View full results | ||||
