| 1st | 15 | Mutou / Turvey | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:47.4560 | 1:47.6380 | 1:47.4560 |
| 2nd | 46 | Motoyama / Takaboshi | Nissan GT-R Nismo GT500 (R35) | Mola | 1:47.5870 | 1:48.1630 | 1:47.5870 |
| 3rd | 12 | Yasuda / de Oliveira | Nissan GT-R Nismo GT500 (R35) | Team Impul | 1:47.9220 | 1:48.0820 | 1:47.9220 |
| 7th | 24 | Sasaki / Yanagida | Nissan GT-R Nismo GT500 (R35) | Kondo Racing | 1:47.9630 | 1:47.9630 | 1:48.6960 |
| 4th | 19 | Sekiguchi / Kunimoto | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:48.0070 | 1:48.0070 | 1:48.1140 |
| 5th | 8 | Matsuura / Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:48.1080 | 1:48.1080 | 1:48.1910 |
| 8th | 38 | Tachikawa / Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:48.1290 | 1:48.1290 | 1:49.3270 |
| 6th | 17 | Tsukakoshi / Kogure | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:48.5340 | 1:48.6750 | 1:48.5340 |
| 9th | 64 | Nakajima / Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:48.6790 | 1:48.6790 | |
| 10th | 6 | Oshima / Caldarelli | Lexus RC F (USC10) | Lexus Team Le Mans Wako's | 1:48.7630 | 1:48.7630 | |
| 11th | 36 | Itou / Cassidy | Lexus RC F (USC10) | Lexus Team Tom's | 1:48.8610 | 1:48.8610 | |
| 12th | 1 | Matsuda / Quintarelli | Nissan GT-R Nismo GT500 (R35) | NISMO | 1:48.8960 | 1:48.8960 | |
| 13th | 100 | Yamamoto / Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:49.1500 | 1:49.1500 | |
| 14th | 37 | Rossiter / Hirakawa | Lexus RC F (USC10) | Lexus Team Tom's | 1:49.1570 | 1:49.1570 | |
| 15th | 39 | Kovalainen / Hirate | Lexus RC F (USC10) | Lexus Team Sard | 1:49.2040 | 1:49.2040 | |
| 19th | 2 | Takahashi / Katou / Makino | Lotus Evora MC (122) | Cars Tokai Dream28 | 1:57.8110 | 1:57.8110 | 1:58.1270 |
| 17th | 18 | Nakayama / Yamada | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:57.8760 | 1:58.9230 | 1:57.8760 |
| 18th | 31 | Saga / Nakayama | Toyota Prius (ZVW50) | Apr | 1:58.0920 | 1:59.6380 | 1:58.0920 |
| 20th | 61 | Iguchi / Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:58.3480 | 1:59.2890 | 1:58.3480 |
| 21st | 25 | Tsuchiya / Matsui / Yamashita | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:58.6080 | 1:59.0690 | 1:58.6080 |
| 25th | 65 | Kurosawa / Gamou | Mercedes-AMG GT3 (197) | K2 R&D Leon Racing | 1:58.9230 | 1:58.9230 | 1:59.4840 |
| 30th | 88 | Orido / Hiramine | Lamborghini Huracán GT3 | JLOC | 1:58.9340 | 1:58.9340 | 2:00.5590 |
| 22nd | 0 | Couto / Tomita | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:58.9470 | 1:59.2110 | 1:58.9470 |
| 23rd | 4 | Taniguchi / Kataoka | Mercedes-AMG GT3 | Goodsmile Racing & Team Ukyo | 1:58.9810 | 1:59.1800 | 1:58.9810 |
| 29th | 26 | Mitsuyama / Motojima / Nakano | Audi R8 LMS Ultra | Team Taisan SARD | 1:59.1790 | 1:59.1790 | 2:00.2350 |
| 24th | 33 | Yamano / Sakamoto | Porsche 991 GT3 R | Excellence Porsche Team KTR | 1:59.2300 | 1:59.6890 | 1:59.2300 |
| 27th | 3 | Hoshino / Mardenborough | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:59.4430 | 1:59.4430 | 1:59.9040 |
| 26th | 63 | Zaugg / Yokomizo | Lamborghini Huracán GT3 | Lamboghini Team Direction | 1:59.7280 | 1:59.8250 | 1:59.7280 |
| 28th | 21 | Lyons / Fujii | Audi R8 LMS | Audi Team Hitotsuyama | 1:59.9490 | 1:59.9490 | 2:00.0200 |
| 31st | 11 | Hiranaka / Wirdheim | Mercedes-AMG GT3 | Gainer | 2:00.3660 | 2:00.3660 | |
| 32nd | 48 | Takamori / Tanaka / Aoki | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:00.5220 | 2:00.5220 | |
| 33rd | 87 | Hosokawa / Satou / Iida | Lamborghini Huracán GT3 | JLOC | 2:00.5300 | 2:00.5300 | |
| 34th | 51 | Tsuduki / Nitta / Wakisaka | Ferrari 488 GT3 | LM Corsa | 2:00.5630 | 2:00.5630 | |
| 35th | 360 | Shibata / Tanaka / Kiyohara | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 2:00.6090 | 2:00.6090 | |
| 36th | 7 | Farfus / Ara / Müller | BMW M6 GT3 (F13) | BMW Team Studie | 2:00.6540 | 2:00.6540 | |
| 37th | 9 | Sakaguchi / Yoshida | Porsche 991 GT3 R | Gulf Racing With Pacific | 2:00.7200 | 2:00.7200 | |
| 38th | 108 | Mineo / Lester / Takeuchi | Lamborghini Huracán GT3 | Lamboghini Team Direction Shift | 2:00.7820 | 2:00.7820 | |
| 39th | 111 | Ueda / Tsuruta / Ishikawa | Mercedes-AMG GT3 | Rn-sports | 2:01.0740 | 2:01.0740 | |
| 40th | 55 | Takagi / Kobayashi | BMW M6 GT3 (F13) | Autobacs Racing Team Aguri | 2:01.1680 | 2:01.1680 | |
| 41st | 22 | Wada / Jounai / Azuma | Mercedes-Benz SLS AMG GT3 | RQ's Motorsports | 2:02.5910 | 2:02.5910 | |
| 42nd | 60 | Iida / Yoshimoto / Farnbacher | Lexus RC F GT3 (USC10) | LM Corsa | 2:06.1360 | 2:06.1360 | |
| 43rd | 30 | Nagai / Sasaki | Toyota Prius (ZVW50) | Apr | 2:09.7390 | 2:09.7390 | |
| 44th | 50 | Yasuoka / Kubo / Kano | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 3:30.9500 | 3:30.9500 | |
| 45th | 5 | Tamanaka / Yamashita / Kageyama | Toyota 86 MC (86/ZN6) | Team Mach | no time | no time | |