| 39 | Kouhei Hirate / Heikki Kovalainen | Lexus RC F (USC10) | Lexus Team Sard | 1:36.4910 |
| 37 | James Rossiter / Ryo Hirakawa | Lexus RC F (USC10) | Lexus Team Tom's | 1:36.7740 |
| 6 | Kazuya Oshima / Andrea Caldarelli | Lexus RC F (USC10) | Lexus Team Le Mans Wako's | 1:36.7760 |
| 19 | Yuuhi Sekiguchi / Yuuji Kunimoto | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:37.1410 |
| 12 | Hironobu Yasuda / Joao Paolo de Oliveira | Nissan GT-R Nismo GT500 (R35) | Team Impul | 1:37.1440 |
| 36 | Daisuke Itou / Nick Cassidy | Lexus RC F (USC10) | Lexus Team Tom's | 1:37.2260 |
| 38 | Yuuji Tachikawa / Hiroaki Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:37.2700 |
| 46 | Satoshi Motoyama / Katsumasa Chiyo | Nissan GT-R Nismo GT500 (R35) | Mola | 1:37.4830 |
| 1 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R Nismo GT500 (R35) | NISMO | 1:37.6350 |
| 17 | Koudai Tsukakoshi / Takashi Kogure | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:37.7410 |
| 8 | Kousuke Matsuura / Tomoki Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:37.7860 |
| 24 | Daiki Sasaki / Masataka Yanagida | Nissan GT-R Nismo GT500 (R35) | Kondo Racing | 1:37.8120 |
| 15 | Hideki Mutou / Tadasuke Makino | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:37.9770 |
| 100 | Naoki Yamamoto / Takuya Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:38.1140 |
| 64 | Daisuke Nakajima / Bertrand Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:39.4240 |
| 31 | Kouki Saga / Yuichi Nakayama | Toyota Prius (ZVW50) | Apr | 1:46.7600 |
| 65 | Haruki Kurosawa / Naoya Gamou | Mercedes-AMG GT3 (197) | K2 R&D Leon Racing | 1:46.8300 |
| 88 | Kazuki Hiramine / Manabu Orido | Lamborghini Huracán GT3 | JLOC | 1:46.8570 |
| 9 | Ryohei Sakaguchi / Hiroki Yoshida | Porsche 991 GT3 R | Gulf Racing With Pacific | 1:46.9420 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | Mercedes-AMG GT3 | Goodsmile Racing & Team Ukyo | 1:46.9610 |
| 25 | Takeshi Tsuchiya / Takamitsu Matsui | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:47.0700 |
| 61 | Takuto Iguchi / Hideki Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:47.1350 |
| 21 | Richard Lyons / Tomonobu Fujii | Audi R8 LMS | Audi Team Hitotsuyama | 1:47.1720 |
| 18 | Yuuki Nakayama / Shin'nosuke Yamada | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:47.3810 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-AMG GT3 | Gainer | 1:47.3920 |
| 26 | Yuya Motojima / Kondo | Audi R8 LMS Ultra | Team Taisan SARD | 1:47.5090 |
| 30 | Hiroaki Nagai / Kota Sasaki | Toyota Prius (ZVW50) | Apr | 1:47.5120 |
| 87 | Shin'ya Hosokawa / Kimiya Satou | Lamborghini Huracán GT3 | JLOC | 1:47.7200 |
| 3 | Kazuki Hoshino / Jann Mardenborough | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:47.7530 |
| 7 | Seiji Ara / Jörg Müller | BMW M6 GT3 (F13) | BMW Team Studie | 1:47.8000 |
| 33 | Naoya Yamano / Jörg Bergmeister | Porsche 991 GT3 R | Excellence Porsche Team KTR | 1:47.8960 |
| 48 | Mitsunori Takaboshi / Takayuki Aoki | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:47.9160 |
| 51 | Akihiro Tsuduki / Morio Nitta | Ferrari 488 GT3 | LM Corsa | 1:47.9670 |
| 0 | André Couto / Ryuichiro Tomita | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:48.0430 |
| 5 | Tetsuji Tamanaka / Masami Kageyama | Toyota 86 MC (86/ZN6) | Team Mach | 1:48.1210 |
| 50 | Hideto Yasuoka / Rintaro Kubo | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 1:48.5880 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | RQ's Motorsports | 1:48.8260 |
| 108 | Kyousuke Mineo / Hironori Takeuchi | Lamborghini Huracán GT3 | Lamboghini Team Direction Shift | 1:48.9040 |
| 111 | Masayuki Ueda / Kazuya Tsuruta | Mercedes-AMG GT3 | Rn-sports | 1:48.9280 |
| 2 | Kazuho Takahashi / Hiroki Katou | Lotus Evora MC (122) | Cars Tokai Dream28 | 1:49.0630 |
| 60 | Akira Iida / Hiroki Yoshimoto | Lexus RC F GT3 (USC10) | LM Corsa | 1:49.1400 |
| 63 | Adrian Zaugg / Naoki Yokomizo | Lamborghini Huracán GT3 | Lamboghini Team Direction | 1:49.5390 |
| 360 | Yuusaku Shibata / Atsushi Tanaka | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:52.6460 |