| 1st | 64 | Nakajima / Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:47.7400 | 1:47.7400 | 1:49.8630 |
| 2nd | 38 | Tachikawa / Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:48.0410 | 1:48.0410 | 1:50.3170 |
| 3rd | 36 | Itou / Rossiter | Lexus RC F (USC10) | Lexus Team Petronas Tom's | 1:48.3490 | 1:48.3490 | 1:50.0230 |
| 4th | 39 | Hirate / Kovalainen | Lexus RC F (USC10) | Lexus Team Sard | 1:48.4320 | 1:48.4320 | 1:51.6530 |
| 5th | 37 | Caldarelli / Hirakawa | Lexus RC F (USC10) | Lexus Team KeePer Tom's | 1:48.5010 | 1:48.5010 | 1:49.7380 |
| 6th | 12 | Yasuda / de Oliveira | Nissan GT-R (R35) | Team Impul | 1:48.6510 | 1:48.6510 | 1:50.2560 |
| 7th | 100 | Yamamoto / Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:48.6550 | 1:48.6550 | 1:49.9810 |
| 8th | 19 | Wakisaka / Sekiguchi | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:48.6910 | 1:48.6910 | 1:53.2630 |
| 9th | 17 | Tsukakoshi / Mutou | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:49.4160 | 1:49.4160 | |
| 10th | 6 | Oshima / Kunimoto | Lexus RC F (USC10) | Lexus Team Le Mans Eneos | 1:49.5330 | 1:49.5330 | |
| 11th | 24 | Sasaki / Krumm | Nissan GT-R (R35) | Kondo Racing | 1:49.6160 | 1:49.6160 | |
| 12th | 1 | Matsuda / Quintarelli | Nissan GT-R (R35) | NISMO | 1:49.7570 | 1:49.7570 | |
| 13th | 46 | Motoyama / Yanagida | Nissan GT-R (R35) | Mola | 1:49.7610 | 1:49.7610 | |
| 14th | 8 | Matsuura / Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:49.9840 | 1:49.9840 | |
| 15th | 15 | Kogure / Turvey | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:51.0970 | 1:51.0970 | |
| 16th | 31 | Saga / Nakayama | Toyota Prius (ZVW30) | Apr | 1:56.2230 | 1:56.2230 | 2:00.6020 |
| 17th | 55 | Takagi / Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:56.9050 | 1:56.9050 | 2:10.0890 |
| 18th | 10 | Couto / Chiyo | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:57.4690 | 1:57.4690 | 2:05.2770 |
| 19th | 11 | Hiranaka / Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:57.8530 | 1:57.8530 | 2:02.5660 |
| 20th | 88 | Orido / Hiramine | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:57.9740 | 1:57.9740 | 2:03.3090 |
| 21st | 0 | Taniguchi / Kataoka | Mercedes-Benz SLS AMG GT3 | Goodsmile Racing & TeamUkyo | 1:58.1930 | 1:58.1930 | 2:02.7520 |
| 22nd | 61 | Iguchi / Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:58.2710 | 1:58.2710 | 2:04.3020 |
| 23rd | 5 | Tamanaka / Mitsuyama | Toyota 86 MC (86/ZN6) | Team Mach | 1:58.5000 | 1:58.5000 | 2:08.3280 |
| 24th | 77 | Yokomizo / Mineo | Ferrari 458 Italia GT3 | Direction Racing | 1:58.6560 | 1:58.6560 | 2:05.7770 |
| 25th | 21 | Lyons / Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:58.7210 | 1:58.7210 | 2:06.6620 |
| 26th | 25 | Tsuchiya / Tanigawa | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:58.8950 | 1:58.8950 | 2:03.2050 |
| 27th | 65 | Kurosawa / Gamou | Mercedes-Benz SLS AMG GT3 (197) | Leon Racing | 1:59.0410 | 1:59.0410 | 2:06.3410 |
| 28th | 33 | Sakamoto / Yamashita | Porsche 997 GT3 R | Porsche Team KTR | 1:59.2050 | 1:59.2050 | 2:03.7940 |
| 29th | 7 | Ara / Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:59.2390 | 1:59.2390 | |
| 30th | 3 | Hoshino / Takaboshi | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:59.3480 | 1:59.3480 | |
| 31st | 20 | Nakayama / Ide | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:59.5420 | 1:59.5420 | |
| 32nd | 87 | Aoki / Satou | Lamborghini Gallardo GT-3 (09-7) | JLOC | 1:59.5770 | 1:59.5770 | |
| 33rd | 51 | Nitta / Wakisaka | BMW Z4 GT3 (E89) | LM Corsa | 1:59.8940 | 1:59.8940 | |
| 34th | 360 | Yoshida / Tanaka | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 2:00.6990 | 2:00.6990 | |
| 35th | 60 | Iida / Yoshimoto | Lexus RC F GT3 (USC10) | LM Corsa | 2:00.9540 | 2:00.9540 | |
| 36th | 22 | Wada / Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motor Sports | 2:01.0370 | 2:01.0370 | |
| 37th | 50 | Kano / Indra-Payoong | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 2:01.1350 | 2:01.1350 | |
| 38th | 48 | Takamori / Tanaka | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:01.1540 | 2:01.1540 | |
| 39th | 111 | Ueda / Tsuruta | Mercedes-Benz SLS AMG GT3 | Rn-sports | 2:01.2350 | 2:01.2350 | |
| 40th | 47 | Inoue / Shibata | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:02.2470 | 2:02.2470 | |
| 41st | 9 | Shirasaka / Sakaguchi | McLaren MP4-12C GT3 | Pacific Racing | 2:02.3270 | 2:02.3270 | |
| 42nd | 2 | Takahashi / Katou | Lotus Evora MC (122) | Cars Tokai Dream28 | 2:02.6740 | 2:02.6740 | |
| 43rd | 30 | Koizumi / Iwasaki | Nissan GT-R Nismo GT3 (R35) | Apr | 2:02.7240 | 2:02.7240 | |