| 1st | 64 | Nakajima / Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:47.589 | 1:47.7850 | 1:52.3010 | 1:47.5890 |
| 2nd | 1 | Matsuda / Quintarelli | Nissan GT-R (R35) | NISMO | 1:47.630 | 1:47.6300 | 1:52.0590 | 1:48.6590 |
| 3rd | 46 | Motoyama / Yanagida | Nissan GT-R (R35) | Mola | 1:47.749 | 1:47.7490 | 1:51.9260 | 1:48.7280 |
| 4th | 38 | Tachikawa / Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:47.782 | 1:47.7820 | 1:52.2130 | 1:47.8190 |
| 5th | 15 | Kogure / Turvey | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:48.117 | 1:48.1170 | 1:52.7520 | 1:48.4630 |
| 6th | 17 | Tsukakoshi / Mutou | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:48.149 | 1:48.1490 | 1:59.6470 | 1:48.7460 |
| 7th | 12 | Yasuda / de Oliveira | Nissan GT-R (R35) | Team Impul | 1:48.217 | 1:48.5000 | 1:51.7900 | 1:48.2170 |
| 8th | 37 | Caldarelli / Hirakawa | Lexus RC F (USC10) | Lexus Team KeePer Tom's | 1:48.258 | 1:48.2580 | 1:51.4530 | 1:48.7300 |
| 9th | 100 | Yamamoto / Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:48.514 | 1:50.0750 | 1:52.4490 | 1:48.5140 |
| 10th | 36 | Itou / Rossiter | Lexus RC F (USC10) | Lexus Team Petronas Tom's | 1:48.569 | 1:48.5690 | 1:51.4350 | 2:10.6370 |
| 11th | 39 | Hirate / Kovalainen / Klien | Lexus RC F (USC10) | Lexus Team Sard | 1:48.615 | 1:48.9840 | 1:51.1770 | 1:48.6150 |
| 12th | 24 | Sasaki / Krumm | Nissan GT-R (R35) | Kondo Racing | 1:48.707 | 1:49.0670 | 1:51.7490 | 1:48.7070 |
| 13th | 19 | Wakisaka / Sekiguchi | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:48.758 | 1:48.7580 | 1:51.9450 | 1:48.7740 |
| 14th | 6 | Oshima / Kunimoto | Lexus RC F (USC10) | Lexus Team Le Mans Eneos | 1:48.991 | no time | 1:59.9590 | 1:48.9910 |
| 15th | 8 | Matsuura / Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:49.014 | 1:49.0140 | 1:51.7320 | 1:49.3760 |
| 16th | 2 | Takahashi / Katou / Hamaguchi | Lotus Evora MC (122) | Cars Tokai Dream28 | 1:58.248 | 1:58.2480 | 2:01.9350 | 1:59.6100 |
| 17th | 10 | Couto / Chiyo / Tomita | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:58.600 | 1:58.6000 | 2:02.1600 | 2:00.5620 |
| 18th | 7 | Ara / Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:58.954 | 1:58.9540 | 2:02.0560 | 1:59.8680 |
| 19th | 61 | Iguchi / Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:59.060 | 1:59.0600 | 2:02.2220 | 2:00.4780 |
| 20th | 31 | Saga / Nakayama / Sasaki | Toyota Prius (ZVW30) | Apr | 1:59.077 | 1:59.0770 | 2:02.8430 | 2:00.6020 |
| 21st | 88 | Orido / Hiramine / Satou | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:59.080 | 1:59.0800 | 2:02.8430 | 2:00.2800 |
| 22nd | 55 | Takagi / Kobayashi / Hukuzumi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:59.204 | 1:59.2040 | 2:05.1270 | 2:01.6320 |
| 23rd | 360 | Yoshida / Tanaka / Narisawa | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:59.299 | 1:59.2990 | 2:14.4390 | 1:59.7660 |
| 24th | 25 | Tsuchiya / Matsui / Tanigawa | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:59.345 | 1:59.3450 | 2:03.8130 | 2:01.7010 |
| 25th | 18 | Nakayama / Asmer / Cassidy | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:59.399 | 1:59.3990 | 2:02.4380 | 2:01.8210 |
| 26th | 21 | Lyons / Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:59.514 | 1:59.5140 | 2:03.3310 | 2:00.0850 |
| 27th | 11 | Hiranaka / Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:59.826 | 1:59.8260 | 2:03.0470 | 2:00.5960 |
| 28th | 77 | Yokomizo / Mineo / Iida | Ferrari 458 Italia GT3 | Direction Racing | 2:00.111 | 2:00.2310 | 2:03.1840 | 2:00.1110 |
| 29th | 5 | Tamanaka / Mitsuyama | Toyota 86 MC (86/ZN6) | Team Mach | 2:00.148 | 2:00.1480 | 2:14.9220 | 2:01.6050 |
| 30th | 3 | Hoshino / Takaboshi / Reip | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:00.274 | 2:00.2960 | 2:02.8670 | 2:00.2740 |
| 31st | 33 | Sakamoto / Yamashita | Porsche 997 GT3 R | Porsche Team KTR | 2:00.274 | 2:00.2740 | 2:03.7900 | 2:00.8610 |
| 32nd | 0 | Taniguchi / Kataoka | Mercedes-Benz SLS AMG GT3 | Goodsmile Racing & TeamUkyo | 2:00.381 | 2:00.4120 | 2:03.2070 | 2:00.3810 |
| 33rd | 51 | Nitta / Wakisaka | BMW Z4 GT3 (E89) | LM Corsa | 2:00.451 | 2:00.4510 | 2:02.8990 | 2:12.7680 |
| 34th | 65 | Kurosawa / Gamou | Mercedes-Benz SLS AMG GT3 (197) | Leon Racing | 2:00.466 | 2:00.4660 | 2:03.0950 | 2:00.5680 |
| 35th | 50 | Kano / Indra-Payoong / Yasuoka | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 2:01.032 | 2:01.0320 | 2:13.9130 | 2:01.7760 |
| 36th | 48 | Takamori / Tanaka / Shibata | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:01.110 | 2:01.1100 | 2:03.7600 | 2:01.5860 |
| 37th | 30 | Koizumi / Iwasaki | Nissan GT-R Nismo GT3 (R35) | Apr | 2:01.181 | 2:01.2120 | 2:03.1920 | 2:01.1810 |
| 38th | 60 | Iida / Yoshimoto / Farnbacher | Lexus RC F GT3 (USC10) | LM Corsa | 2:01.357 | 2:01.3570 | 2:03.3230 | 2:03.7540 |
| 39th | 22 | Wada / Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motor Sports | 2:01.436 | 2:01.4360 | 2:03.4610 | 2:02.1330 |
| 40th | 111 | Ueda / Tsuruta / Ikegami | Mercedes-Benz SLS AMG GT3 | Rn-sports | 2:01.588 | 2:01.5880 | 2:04.7380 | 2:05.3840 |
| 41st | 87 | Aoki / Yamanishi / Kuroda | Lamborghini Gallardo GT-3 (09-7) | JLOC | 2:01.815 | 2:02.0770 | 2:05.1130 | 2:01.8150 |
| 42nd | 9 | Shirasaka / Sakaguchi / Yamawaki | McLaren MP4-12C GT3 | Pacific Racing | 2:01.857 | 2:01.8570 | 2:05.1920 | 2:02.3880 |
| 43rd | 86 | Mamerow / Hosokawa / Katou | Audi R8 LMS Ultra | Audi Team Racing Tech | 2:03.833 | no time | 2:03.8330 | 2:04.3330 |