The Nakajima Racing driver, who is set to remain with the team for a third season next year, posted a best time of 1m35.613s with around 15 minutes remaining in an extended 2hr10min afternoon session to go fastest.
Kondo Racing's Kenta Yamashita made a last-minute jump up to second with a time just 0.051s shy of Yamamoto's benchmark, while Ryo Hirakawa was third-fastest for Impul.
Best of the rookies was Red Bull junior driver Liam Lawson, who was ninth-fastest in the afternoon session and 10th overall in the sole Team Mugen car, the #15 machine raced this year by Ukyo Sasahara.
The New Zealander completed 63 laps across the course of the day's running, which was interrupted by no fewer than seven red flags, with a best lap 0.897s off the pace on his first day aboard the Dallara SF19.
Nakajima Racing newcomer Ren Sato topped the opening session with a best time of 1m36.117s before suffering a crash at Turn 2, which caused the fifth and final stoppage of the morning's running.
The damage was sufficiently light that he was able to rejoin the field for the afternoon, only to suffer a second - and more serious-looking - shunt at the second Degner Curve that brought his day to an early end.
Sato's morning time was still enough for him to end up sixth-fastest overall behind Sho Tsuboi (Inging) and Kamui Kobayashi (KCMG).
Both Hirakawa and Kobayashi will sit out the second day of the test as they head to the FIA Prize Giving in Italy to celebrate Toyota's success in the FIA World Endurance Championship.
Giuliano Alesi was ninth-fastest for TOM'S as he fights for his Super Formula survival against Sasahara, who will take over at the wheel of the Toyota squad's #36 car on Thursday.
Second-best of the rookies was Dandelion Racing's Kakunoshin Ota, who appears to be auditioning for a place in the team's 2023 line-up alongside the absent Tadasuke Makino.
Having been responsible for the fourth red flag of the morning with a spin at the hairpin, Ota recovered in the afternoon to go 12th-fastest overall, five places behind teammate Hiroki Otsu.
Of the other newcomers, Igor Fraga was 14th-fastest for Impul, Cem Bolukbasi was 17th-fastest in his Servus Japan-run car, while HPD scholarship winner Raoul Hyman brought up the rear in 20th for B-Max Racing.
Kazuto Kotaka, who replaces Sacha Fenestraz at Kondo Racing for 2023, suffered a spin at Dunlop corner that caused the afternoon's first stoppage on his way to the 16th-fastest time of the day.
Atsushi Miyake was 18th aboard the Drago Corse machine that he will hand over to regular driver Nirei Fukuzumi for Thursday.
In Super Formula Lights testing, TOM'S driver Seita Nonaka set the pace in all three sessions, ending up on a best time of 1m49.896s. Honda protege Shun Koide was his nearest rival, 0.084s off the pace for Toda Racing.
Suzuka testing Day 1 results:
| Pos. | No. | Driver | Team/Engine | Morning | Afternoon |
|---|---|---|---|---|---|
| 1 | 64 |
 Naoki Yamamoto |
Nakajima/Honda | 1'38.060 | 1'35.613 |
| 2 | 3 |
Kenta Yamashita |
Kondo/Toyota | 1'38.346 | 1'35.664 |
| 3 | 20 |
Ryo Hirakawa |
Impul/Toyota | 1'37.314 | 1'35.773 |
| 4 | 38 |
Sho Tsuboi |
Inging/Toyota | 1'39.500 | 1'35.866 |
| 5 | 7 |
Kamui Kobayashi |
KCMG/Toyota | 1'38.443 | 1'36.077 |
| 6 | 65 |
Ren Sato |
Nakajima/Honda | 1'36.117 | 1'37.539 |
| 7 | 5 |
Hiroki Otsu |
Dandelion/Honda | 1'37.463 | 1'36.200 |
| 8 | 37 |
Ritomo Miyata |
TOM'S/Toyota | 1'38.673 | 1'37.412 |
| 9 | 36 |
 Giuliano Alesi |
TOM'S/Toyota | 1'39.173 | 1'36.428 |
| 10 | 15 |
 Liam Lawson |
Mugen/Honda | 1'39.263 | 1'36.510 |
| 11 | 18 |
Yuji Kunimoto |
KCMG/Toyota | 1'38.977 | 1'36.654 |
| 12 | 6 |
Kakunoshin Ota |
Dandelion/Honda | 1'40.487 | 1'36.856 |
| 13 | 14 |
Kazuya Oshima |
Rookie/Toyota | 1'37.420 | 1'37.104 |
| 14 | 19 |
 Igor Fraga |
Impul/Toyota | 1'39.362 | 1'37.120 |
| 15 | 39 |
Sena Sakaguchi |
Inging/Toyota | 1'38.292 | 1'37.147 |
| 16 | 4 |
Kazuto Kotaka |
Kondo/Toyota | 1'38.524 | 1'37.719 |
| 17 | 33 |
 Cem Bolukbasi |
Servus/Honda* | 1'40.289 | 1'38.354 |
| 18 | 12 |
Atsushi Miyake |
Drago Corse/Honda | 1'38.909 | 1'38.393 |
| 19 | 50 |
Nobuharu Matsushita |
B-Max/Honda | 1'38.995 | 1'38.537 |
| 20 | 51 |
 Raoul Hyman |
B-Max/Honda | 1'42.057 | 1'38.777 |
* car officially entered as 'Team TBD'
