| 1st | 19 | Wakisaka / Sekiguchi | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:41.384 | 1:48.6910 | 1:41.3840 | 1:51.0530 | 1:48.1370 |
| 2nd | 6 | Oshima / Kunimoto | Lexus RC F (USC10) | Lexus Team Le Mans Eneos | 1:41.461 | 1:49.5330 | 1:41.4610 | 1:50.9250 | 1:47.5830 |
| 3rd | 38 | Tachikawa / Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:41.523 | 1:48.0410 | 1:41.5230 | 1:49.6760 | 1:47.0960 |
| 4th | 100 | Yamamoto / Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:41.531 | 1:48.6550 | 1:41.5310 | 1:49.1140 | 1:47.2930 |
| 5th | 24 | Sasaki / Krumm | Nissan GT-R (R35) | Kondo Racing | 1:41.569 | 1:49.6160 | 1:41.5690 | 1:51.5910 | 1:48.2130 |
| 6th | 15 | Kogure / Turvey | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:41.574 | 1:51.0970 | 1:41.5740 | 1:50.2150 | 1:48.8750 |
| 7th | 1 | Matsuda / Quintarelli | Nissan GT-R (R35) | NISMO | 1:41.606 | 1:49.7570 | 1:41.6060 | 1:50.7470 | 1:46.9080 |
| 8th | 12 | Yasuda / de Oliveira | Nissan GT-R (R35) | Team Impul | 1:41.654 | 1:48.6510 | 1:41.6540 | 1:49.7440 | 1:47.8460 |
| 9th | 17 | Tsukakoshi / Mutou | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:41.685 | 1:49.4160 | 1:41.6850 | 1:50.0260 | 1:47.4730 |
| 10th | 37 | Caldarelli / Hirakawa | Lexus RC F (USC10) | Lexus Team KeePer Tom's | 1:41.759 | 1:48.5010 | 1:41.7590 | 1:49.9680 | 1:47.4400 |
| 11th | 8 | Matsuura / Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:41.833 | 1:49.9840 | 1:41.8330 | 1:50.0480 | 1:48.0940 |
| 12th | 39 | Hirate / Kovalainen | Lexus RC F (USC10) | Lexus Team Sard | 1:41.884 | 1:48.4320 | 1:41.8840 | 1:50.1620 | 1:48.4290 |
| 13th | 64 | Nakajima / Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:42.235 | 1:47.7400 | 1:42.2350 | 1:50.1920 | 1:46.6310 |
| 14th | 46 | Motoyama / Yanagida | Nissan GT-R (R35) | Mola | 1:44.277 | 1:49.7610 | 1:44.2770 | 1:52.9910 | 1:48.5440 |
| 15th | 36 | Itou / Rossiter | Lexus RC F (USC10) | Lexus Team Petronas Tom's | 1:47.640 | 1:48.3490 | 1:50.0340 | 1:50.1230 | 1:47.6400 |
| 16th | 31 | Saga / Nakayama | Toyota Prius (ZVW30) | Apr | 1:49.434 | 1:56.2230 | 1:49.4340 | 1:57.3630 | 1:55.9540 |
| 17th | 2 | Takahashi / Katou | Lotus Evora MC (122) | Cars Tokai Dream28 | 1:49.753 | 2:02.6740 | 1:49.7530 | 1:59.3020 | 1:57.4010 |
| 18th | 10 | Couto / Chiyo | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:49.782 | 1:57.4690 | 1:49.7820 | 1:59.6580 | 1:59.0600 |
| 19th | 0 | Taniguchi / Kataoka | Mercedes-Benz SLS AMG GT3 | Goodsmile Racing & TeamUkyo | 1:49.983 | 1:58.1930 | 1:49.9830 | 1:57.5870 | 1:56.8250 |
| 20th | 65 | Kurosawa / Gamou | Mercedes-Benz SLS AMG GT3 (197) | Leon Racing | 1:50.158 | 1:59.0410 | 1:50.1580 | 1:59.1710 | 1:57.3950 |
| 21st | 88 | Orido / Hiramine | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:50.315 | 1:57.9740 | 1:50.3150 | 1:59.1910 | 1:56.3380 |
| 22nd | 25 | Tsuchiya / Tanigawa | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:50.474 | 1:58.8950 | 1:50.4740 | 2:00.3110 | 1:57.1840 |
| 23rd | 61 | Iguchi / Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:50.659 | 1:58.2710 | 1:50.6590 | 2:00.0570 | 1:57.5930 |
| 24th | 77 | Yokomizo / Mineo | Ferrari 458 Italia GT3 | Direction Racing | 1:50.800 | 1:58.6560 | 1:50.8000 | 2:00.0050 | 1:58.4640 |
| 25th | 55 | Takagi / Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:51.249 | 1:56.9050 | 1:51.2490 | 2:01.2450 | 1:57.1010 |
| 26th | 7 | Ara / Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:51.366 | 1:59.2390 | 1:51.3660 | 1:59.5610 | 1:58.0370 |
| 27th | 21 | Lyons / Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:51.441 | 1:58.7210 | 1:51.4410 | 1:59.5380 | 1:57.1780 |
| 28th | 11 | Hiranaka / Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:51.457 | 1:57.8530 | 1:51.4570 | 1:57.9970 | 1:56.4230 |
| 29th | 33 | Sakamoto / Yamashita | Porsche 997 GT3 R | Porsche Team KTR | 1:51.699 | 1:59.2050 | 1:51.6990 | 1:58.8200 | 1:57.1880 |
| 30th | 51 | Nitta / Wakisaka | BMW Z4 GT3 (E89) | LM Corsa | 1:51.820 | 1:59.8940 | 1:51.8200 | 2:01.8850 | 1:59.5450 |
| 31st | 87 | Aoki / Satou | Lamborghini Gallardo GT-3 (09-7) | JLOC | 1:52.082 | 1:59.5770 | 1:52.0820 | 1:59.9550 | 1:58.6210 |
| 32nd | 48 | Takamori / Tanaka | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:52.145 | 2:01.1540 | 1:52.1450 | 2:00.8650 | 1:59.4430 |
| 33rd | 22 | Wada / Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motor Sports | 1:52.305 | 2:01.0370 | 1:52.3050 | 2:01.7510 | 1:59.7680 |
| 34th | 30 | Koizumi / Iwasaki | Nissan GT-R Nismo GT3 (R35) | Apr | 1:52.568 | 2:02.7240 | 1:52.5680 | 2:02.1400 | 2:00.7860 |
| 35th | 111 | Ueda / Tsuruta | Mercedes-Benz SLS AMG GT3 | Rn-sports | 1:53.005 | 2:01.2350 | 1:53.0050 | 2:01.8050 | 1:59.8940 |
| 36th | 50 | Kano / Indra-Payoong | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 1:53.046 | 2:01.1350 | 1:53.0460 | 2:01.7110 | 1:59.6850 |
| 37th | 47 | Inoue / Shibata | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:53.061 | 2:02.2470 | 1:53.0610 | 2:03.1900 | 2:00.5090 |
| 38th | 60 | Iida / Yoshimoto | Lexus RC F GT3 (USC10) | LM Corsa | 1:53.389 | 2:00.9540 | 1:53.3890 | 2:02.3530 | 1:59.7180 |
| 39th | 360 | Yoshida / Tanaka | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:53.613 | 2:00.6990 | 1:53.6130 | 2:00.3600 | 1:58.3760 |
| 40th | 5 | Tamanaka / Mitsuyama | Toyota 86 MC (86/ZN6) | Team Mach | 1:54.100 | 1:58.5000 | 1:54.1000 | 2:06.1100 | 1:58.7530 |
| 41st | 3 | Hoshino / Takaboshi | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:57.238 | 1:59.3480 | | 1:59.6040 | 1:57.2380 |
| 42nd | 20 | Nakayama / Ide | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:58.699 | 1:59.5420 | | 2:00.7900 | 1:58.6990 |
| 43rd | 9 | Shirasaka / Sakaguchi | McLaren MP4-12C GT3 | Pacific Racing | 1:59.346 | 2:02.3270 | 2:02.7830 | 2:01.2990 | 1:59.3460 |