| 1st | 1 | Matsuda / Quintarelli | Nissan GT-R (R35) | NISMO | 1:47.6300 | 1:48.3940 | 1:47.6300 |
| 2nd | 46 | Motoyama / Yanagida | Nissan GT-R (R35) | Mola | 1:47.7490 | 1:47.7490 | 1:48.0420 |
| 3rd | 38 | Tachikawa / Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:47.7820 | 1:47.9410 | 1:47.7820 |
| 4th | 64 | Nakajima / Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:47.7850 | 1:48.0220 | 1:47.7850 |
| 5th | 15 | Kogure / Turvey | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:48.1170 | 1:48.1170 | 1:48.7180 |
| 6th | 17 | Tsukakoshi / Mutou | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:48.1490 | 1:48.1490 | 2:12.7240 |
| 7th | 37 | Caldarelli / Hirakawa | Lexus RC F (USC10) | Lexus Team KeePer Tom's | 1:48.2580 | 1:48.2580 | 1:48.6650 |
| 8th | 12 | Yasuda / de Oliveira | Nissan GT-R (R35) | Team Impul | 1:48.5000 | 1:48.5670 | 1:48.5000 |
| 9th | 36 | Itou / Rossiter | Lexus RC F (USC10) | Lexus Team Petronas Tom's | 1:48.5690 | 1:48.5690 | |
| 10th | 19 | Wakisaka / Sekiguchi | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:48.7580 | 1:48.7580 | |
| 11th | 39 | Hirate / Kovalainen / Klien | Lexus RC F (USC10) | Lexus Team Sard | 1:48.9840 | 1:48.9840 | |
| 12th | 8 | Matsuura / Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:49.0140 | 1:49.0140 | |
| 13th | 24 | Sasaki / Krumm | Nissan GT-R (R35) | Kondo Racing | 1:49.0670 | 1:49.0670 | |
| 14th | 100 | Yamamoto / Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:50.0750 | 1:50.0750 | |
| 15th | 2 | Takahashi / Katou / Hamaguchi | Lotus Evora MC (122) | Cars Tokai Dream28 | 1:58.2480 | 1:59.9610 | 1:58.2480 |
| 16th | 10 | Couto / Chiyo / Tomita | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:58.6000 | 1:59.8390 | 1:58.6000 |
| 17th | 7 | Ara / Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:58.9540 | 2:00.1950 | 1:58.9540 |
| 18th | 61 | Iguchi / Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:59.0600 | 1:59.2400 | 1:59.0600 |
| 19th | 31 | Saga / Nakayama / Sasaki | Toyota Prius (ZVW30) | Apr | 1:59.0770 | 1:59.0770 | 1:59.5920 |
| 20th | 88 | Orido / Hiramine / Satou | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:59.0800 | 1:59.3160 | 1:59.0800 |
| 21st | 55 | Takagi / Kobayashi / Hukuzumi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:59.2040 | 1:59.9060 | 1:59.2040 |
| 22nd | 360 | Yoshida / Tanaka / Narisawa | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:59.2990 | 1:59.2990 | 2:04.3290 |
| 23rd | 25 | Tsuchiya / Matsui / Tanigawa | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:59.3450 | 1:59.5070 | 1:59.3450 |
| 24th | 18 | Nakayama / Asmer / Cassidy | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:59.3990 | 1:59.3990 | 1:59.4870 |
| 25th | 21 | Lyons / Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:59.5140 | 1:59.5140 | 2:00.0130 |
| 26th | 11 | Hiranaka / Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:59.8260 | 1:59.8260 | 2:00.0970 |
| 27th | 5 | Tamanaka / Mitsuyama | Toyota 86 MC (86/ZN6) | Team Mach | 2:00.1480 | 2:00.1480 | 2:01.6430 |
| 28th | 77 | Yokomizo / Mineo / Iida | Ferrari 458 Italia GT3 | Direction Racing | 2:00.2310 | 2:00.2310 | |
| 29th | 33 | Sakamoto / Yamashita | Porsche 997 GT3 R | Porsche Team KTR | 2:00.2740 | 2:00.2740 | |
| 30th | 3 | Hoshino / Takaboshi / Reip | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:00.2960 | 2:00.2960 | |
| 31st | 0 | Taniguchi / Kataoka | Mercedes-Benz SLS AMG GT3 | Goodsmile Racing & TeamUkyo | 2:00.4120 | 2:00.4120 | |
| 32nd | 51 | Nitta / Wakisaka | BMW Z4 GT3 (E89) | LM Corsa | 2:00.4510 | 2:00.4510 | |
| 33rd | 65 | Kurosawa / Gamou | Mercedes-Benz SLS AMG GT3 (197) | Leon Racing | 2:00.4660 | 2:00.4660 | |
| 34th | 50 | Kano / Indra-Payoong / Yasuoka | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 2:01.0320 | 2:01.0320 | |
| 35th | 48 | Takamori / Tanaka / Shibata | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:01.1100 | 2:01.1100 | |
| 36th | 30 | Koizumi / Iwasaki | Nissan GT-R Nismo GT3 (R35) | Apr | 2:01.2120 | 2:01.2120 | |
| 37th | 60 | Iida / Yoshimoto / Farnbacher | Lexus RC F GT3 (USC10) | LM Corsa | 2:01.3570 | 2:01.3570 | |
| 38th | 22 | Wada / Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motor Sports | 2:01.4360 | 2:01.4360 | |
| 39th | 111 | Ueda / Tsuruta / Ikegami | Mercedes-Benz SLS AMG GT3 | Rn-sports | 2:01.5880 | 2:01.5880 | |
| 40th | 9 | Shirasaka / Sakaguchi / Yamawaki | McLaren MP4-12C GT3 | Pacific Racing | 2:01.8570 | 2:01.8570 | |
| 41st | 87 | Aoki / Yamanishi / Kuroda | Lamborghini Gallardo GT-3 (09-7) | JLOC | 2:02.0770 | 2:02.0770 | |
| 15th | 6 | Oshima / Kunimoto | Lexus RC F (USC10) | Lexus Team Le Mans Eneos | no time | no time | |
| 44th | 86 | Mamerow / Hosokawa / Katou | Audi R8 LMS Ultra | Audi Team Racing Tech | no time | no time | |