Fenestraz was the only driver to dip beneath the 1m21 bracket in five-and-a-half hours of running on Wednesday, setting his best lap of 1m20.953s in the dying moments of the afternoon session.
That was enough to beat Sho Tsuboi to the top time by 0.194s, albeit with a red flag curtailing the session a minute or so early and preventing some drivers from completing their best laps.
After an opening day lost to rain and snow, the two-hour morning session passed without incident, with Yuhi Sekiguchi (Impul) and rookie Ren Sato (Team Goh) setting identical times of 1m21.815s at the top of the order.
All 21 drivers set their best times in the afternoon, which was extended by 30 minutes but interrupted by three red flags.
Fenestraz hit the top of the timesheets after the first of these interruptions, caused by Sato coming to a halt at Turn 3 with an apparent mechanical issue, as he posted a 1m21.335s.
That was then bested by Tsuboi's 1m21.147s effort following the second stoppage, as Kamui Kobayashi (KCMG) spun exiting the penultimate corner.
Most drivers went for attack laps at the end of the session, with Fenestraz usurping Tsuboi at the head of the timesheets just moments before Yuji Kunimoto (KCMG) caused the final red flag with an off at Turn 10.
Behind Fenestraz and Tsuboi, Ritomo Miyata was third-fastest for TOM'S, 0.297s off the pace, ahead of Sekiguchi in the best of the Impul machines.
Toyota-powered cars locked out the top four, with Honda's best representative being reigning champion Tomoki Nojiri (Mugen) in fifth on a 1m21.365s, some four tenths slower than Fenestraz.
Giuliano Alesi was sixth in the second TOM'S car ahead of Dandelion newcomer Hiroki Otsu and Fenestraz's Kondo Racing teammate Kenta Yamashita.
Completing the top 10 were Ryo Hirakawa (Impul) and Nobuharu Matsushita (B-Max Racing).
Having jointly topped the morning timesheets, Sato could do no better than 15th in the afternoon, returning to the track after his stoppage, a place behind Goh teammate and fellow rookie Atsushi Miyake.
Nakajima Racing suffered a low-key day with Toshiki Oyu way down in 18th, a second off the pace, followed by three-time champion Naoki Yamamoto in 19th.
Super Formula Lights was also in action during the break between the two Super Formula sessions. Setting the pace was Helm Motorsports driver Reiji Hiraki, ahead of Honda junior Kakunoshin Ota for Toda Racing and TOM'S man Seita Nonaka.
Fuji will host the opening round of the Super Formula season on April 8-10, with the season set to kick off with a double-header.
Fuji testing times:
| Pos. | Driver | Team/Engine | Morning | Afternoon |
|---|---|---|---|---|
| 1 |
 Sacha Fenestraz | Kondo/Toyota | 1'22.019 | 1'20.953 |
| 2 |
 Sho Tsuboi | Inging/Toyota | 1'22.093 | 1'21.147 |
| 3 |
Ritomo Miyata | TOM'S/Toyota | 1'23.308 | 1'21.250 |
| 4 |
Yuhi Sekiguchi | Impul/Toyota | 1'21.815 | 1'21.316 |
| 5 |
Tomoki Nojiri | Nojiri/Mugen | 1'22.242 | 1'21.365 |
| 6 |
Giuliano Alesi | TOM'S/Toyota | 1'22.244 | 1'21.418 |
| 7 |
Hiroki Otsu | Dandelion/Honda | 1'22.248 | 1'21.439 |
| 8 |
Kenta Yamashita | Kondo/Toyota | 1'22.488 | 1'21.441 |
| 9 |
Ryo Hirakawa | Impul/Toyota | 1'21.869 | 1'21.487 |
| 10 |
Nobuharu Matsushita | B-Max/Honda | 1'22.546 | 1'21.576 |
| 11 |
Tadasuke Makino | Dandelion/Honda | 1'21.914 | 1'21.631 |
| 12 |
Ukyo Sasahara | Mugen/Honda | 1'22.198 | 1'21.651 |
| 13 |
| KCMG/Toyota | 1'23.135 | 1'21.767 |
| 14 |
| Goh/Honda | 1'22.285 | 1'21.799 |
| 15 |
| Goh/Honda | 1'21.815 | 1'21.803 |
| 16 |
| Rookie/Toyota | 1'22.844 | 1'21.844 |
| 17 |
| Inging/Toyota | 1'21.988 | 1'21.906 |
| 18 |
| Nakajima/Honda | 1'22.681 | 1'21.980 |
| 19 |
| Nakajima/Honda | 1'22.543 | 1'22.147 |
| 20 |
| Drago Corse/Honda | 1'22.800 | 1'22.167 |
| 21 |
| KCMG/Toyota | 1'22.611 | 1'22.211 |
