Impul man Sekiguchi claimed the top spot with a 1m35.951s to give the Toyota-powered contingent its first pole of the season, also ending a run of four poles for Nojiri and five for the Mugen Honda team.
Owing to poor weather conditions, the usual two-part knockout qualifying format was abandoned in favour of a single 30-minute session to decide the grid, with the track staying wet throughout.
The top three qualifying times all came early in the session before a crash for Kamui Kobayashi (KCMG) at the Turn 15 left-hander after just seven minutes brought out the first of three red flags.
Almost nine tenths behind Sekiguchi in second was Inging's Sho Tsuboi on a 1m36.858s, while Nojiri's best time of 1m37.240s still allowed him to extended his points lead with a single bonus point for third.
With the rain intensifying in the 10-minute delay, improvements were few and far between - Sena Sakaguchi (Inging)'s effort of 1m37.278s to jump up to fourth being a notable exception - until the second stoppage was triggered with just over six minutes left as Ritomo Miyata (TOM'S) coasted to a halt at the outside of Turn 13.
Action resumed for one final time after that, but with the track conditions even worse by that time, there were no further improvements until the red flags came out again with around 90 seconds to go.
The session was not resumed thereafter, guaranteeing Sekiguchi and Impul its first pole since last year's Sugo round, and Tsuboi by far his best grid slot of a miserable season so far.
Sekiguchi's team-mate Ryo Hirakawa had qualified sixth behind the Dandelion Racing machine of Hiroki Otsu, but lost his best lap owing to a track limits infringement and will instead start 11th. Nojiri's bonus point means Hirakawa is now 18 points behind in the drivers' standings.
Tadasuke Makino had qualified seventh but will now join team-mate Otsu on the third row in sixth, while the other realistic title contender, Sugo winner Sacha Fenestraz (Kondo Racing), was promoted to seventh but is now 25 points down on Nojiri.
With Miyata dropping to the rear for causing the second red flag, Nirei Fukuzumi (Drago Corse), Suzuka winner Nobuharu Matsushita (B-Max Racing) and Toshiki Oyu (Nakajima Racing) complete the top 10.
Ukyo Sasahara (Mugen), who scored the first pole of the season at Fuji back in April, qualified down in 16th but was promoted to 13th after Hirakawa, Kenta Yamashita (Kondo) and Ren Sato (Team Goh) all lost their best laps, one place ahead of the struggling Giuliano Alesi (TOM'S).
Sunday's Fuji race is slated to get underway at 14:30 local time (GMT +9).
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Super Formula Fuji - qualifying results:
| Cla | Driver | Team | Time | Gap |
|---|---|---|---|---|
| 1 |
 Yuhi Sekiguchi | Team Impul | 1'35.951 | |
| 2 |
Sho Tsuboi | P.MU/CERUMO･INGING | 1'36.858 | 0.907 |
| 3 |
Tomoki Nojiri | Team Mugen | 1'37.240 | 1.289 |
| 4 |
Sena Sakaguchi | P.MU/CERUMO･INGING | 1'37.278 | 1.327 |
| 5 |
Hiroki Otsu | Dandelion Racing | 1'37.352 | 1.401 |
| 6 |
Ryo Hirakawa | Team Impul | 1'37.518 | 1.567 |
| 7 |
Tadasuke Makino | Dandelion Racing | 1'37.563 | 1.612 |
| 8 |
Ritomo Miyata | Kuo VANTELIN TEAM TOM’S | 1'37.789 | 1.838 |
| 9 |
 Sacha Fenestraz | Kondo Racing | 1'37.809 | 1.858 |
| 10 |
Nirei Fukuzumi | ThreeBond Drago CORSE | 1'37.885 | 1.934 |
| 11 |
Nobuharu Matsushita | B-Max Racing Team | 1'37.984 | 2.033 |
| 12 |
Kenta Yamashita | Kondo Racing | 1'38.105 | 2.154 |
| 13 |
Toshiki Oyu | TCS Nakajima Racing | 1'38.258 | 2.307 |
| 14 |
Atsushi Miyake | Team Goh | 1'38.435 | 2.484 |
| 15 |
Ren Sato | Team Goh | 1'38.998 | 3.047 |
| 16 |
Ukyo Sasahara | Team Mugen | 1'39.060 | 3.109 |
| 17 |
Giuliano Alesi | Kuo VANTELIN TEAM TOM’S | 1'39.329 | 3.378 |
| 18 |
Naoki Yamamoto | TCS Nakajima Racing | 1'40.055 | 4.104 |
| 19 |
Yuji Kunimoto | KCMG | 1'40.356 | 4.405 |
| 20 |
Kazuya Oshima | docomo business ROOKIE | 1'40.773 | 4.822 |
| 21 |
Kamui Kobayashi | KCMG | ||
| View full results | ||||
