| 46 | Satoshi Motoyama / Katsumasa Chiyo | Nissan GT-R Nismo GT500 (R35) | Mola | 1:37.2240 |
| 23 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R Nismo GT500 (R35) | NISMO | 1:37.3450 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus LC500 (URZ100) | Lexus Team au Tom's | 1:37.3590 |
| 17 | Koudai Tsukakoshi / Takashi Kogure | Honda NSX-GT (NC1) | Keihin Real Racing | 1:37.3610 |
| 37 | Ryō Hirakawa / Nick Cassidy | Lexus LC500 (URZ100) | Lexus Team KeePer Tom's | 1:37.5360 |
| 24 | Daiki Sasaki / Joao Paolo de Oliveira | Nissan GT-R Nismo GT500 (R35) | Kondo Racing | 1:37.5720 |
| 6 | Kazuya Oshima / Andrea Caldarelli | Lexus LC500 (URZ100) | Lexus Team Le Mans Wako's | 1:37.7950 |
| 100 | Naoki Yamamoto / Takuya Izawa | Honda NSX-GT (NC1) | Team Kunimitsu | 1:37.8410 |
| 38 | Yuuji Tachikawa / Hiroaki Ishiura | Lexus LC500 (URZ100) | Lexus Team Zent Cerumo | 1:37.8580 |
| 12 | Hironobu Yasuda / Jann Mardenborough | Nissan GT-R Nismo GT500 (R35) | Team Impul | 1:37.9800 |
| 1 | Heikki Kovalainen / Kouhei Hirate | Lexus LC500 (URZ100) | Lexus Team SARD | 1:38.0620 |
| 8 | Tomoki Nojiri / Takashi Kobayashi | Honda NSX-GT (NC1) | Autobacs Racing Team Aguri | 1:38.1640 |
| 16 | Hideki Mutou / Daisuke Nakajima | Honda NSX-GT (NC1) | Team Mugen | 1:38.7060 |
| 64 | Kousuke Matsuura / Bertrand Baguette | Honda NSX-GT (NC1) | Nakajima Racing | 1:38.7350 |
| 19 | Yuuhi Sekiguchi / Yuuji Kunimoto | Lexus LC500 (URZ100) | Lexus Team WedsSport Bandoh | 1:39.0660 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | Mercedes-AMG GT3 (C190) | Goodsmile Racing & Team Ukyo | 1:46.8250 |
| 88 | Manabu Orido / Kazuki Hiramine | Lamborghini Huracán GT3 | JLOC | 1:47.3370 |
| 25 | Takamitsu Matsui / Kenta Yamashita | Toyota 86 MC (ZN6) | Vivac Team Tsuchiya | 1:47.4110 |
| 18 | Yuuki Nakayama / Shintarou Kawabata | Toyota 86 MC (ZN6) | Team Upgarage With Bandoh | 1:47.5520 |
| 65 | Haruki Kurosawa / Naoya Gamou | Mercedes-AMG GT3 (C190) | K2 R&D Leon Racing | 1:47.5710 |
| 9 | Jono Lester / Kyousuke Mineo | Porsche 991 GT3 R | Pacific with Gulf Racing | 1:47.6500 |
| 55 | Shinichi Takagi / Sean Walkinshaw | BMW M6 GT3 (F13) | Autobacs Racing Team Aguri | 1:47.6590 |
| 7 | Seiji Ara / Jörg Müller | BMW M6 GT3 (F13) | BMW Team Studie | 1:47.7290 |
| 2 | Kazuho Takahashi / Hiroki Katou | Lotus Evora MC (122) | Cars Tokai Dream28 | 1:47.7890 |
| 51 | Yuichi Nakayama / Syou Tsuboi | Lexus RC F GT3 (USC10) | LM Corsa | 1:47.8380 |
| 33 | Tomonobu Fujii / Sven Müller | Porsche 991 GT3 R | D'station Racing | 1:47.8730 |
| 61 | Takuto Iguchi / Hideki Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:47.8880 |
| 5 | Natsu Sakaguchi / Kiyoto Fujinami | Toyota 86 MC (ZN6) | Team Mach | 1:47.9670 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-AMG GT3 (C190) | Gainer | 1:47.9960 |
| 60 | Akira Iida / Hiroki Yoshimoto | Lexus RC F GT3 (USC10) | LM Corsa | 1:48.0590 |
| 3 | Kazuki Hoshino / Mitsunori Takaboshi | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:48.2730 |
| 111 | Keishi Ishikawa / Ryousei Yamashita | Mercedes-AMG GT3 (C190) | Rn-sports | 1:48.3620 |
| 87 | Shin'ya Hosokawa / Kimiya Satou | Lamborghini Huracán GT3 | JLOC | 1:48.3640 |
| 31 | Kouki Saga / Rintaro Kubo | Toyota Prius (ZVW51) | Apr | 1:48.5100 |
| 26 | Shin'nosuke Yamada / Jake Parsons | Audi R8 LMS (AS4FAFG3) | Team Taisan SARD | 1:48.5410 |
| 10 | Ryuichiro Tomita / Hiroki Yoshida | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:48.5550 |
| 117 | Yuuji Ide / Ryohei Sakaguchi | Bentley Continental GT3 (BGT3 01) | EIcars Bentley TTO | 1:48.6890 |
| 30 | Hiroaki Nagai / Kota Sasaki | Toyota Prius (ZVW51) | Apr | 1:48.7220 |
| 52 | Taku Bamba / Shigekazu Wakisaka | Toyota Mark X MC (GRX133) | Saitama Toyopet Green Brave | 1:48.7350 |
| 50 | Akihiro Tsuduki / Morio Nitta | Ferrari 488 GT3 (F142M) | Inging & Arnage Racing | 1:48.7530 |
| 360 | Yuusaku Shibata / Takayuki Aoki | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:49.0090 |
| 48 | Hiroshi Takamori / Masaki Tanaka | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:49.2800 |
| 35 | Nattavude Charoensukhawatana / Nattapong Hortongkum | Toyota 86 MC (ZN6) | Panther Team Thailand | 1:49.9140 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motor Sports | 1:50.0060 |