| 1st | 46 | Motoyama / Yanagida | Nissan GT-R (R35) | Mola | 1:48.629 | 1:48.6290 | 1:52.5680 | 1:53.5030 | 1:50.6120 |
| 2nd | 36 | Nakajima / Rossiter | Lexus RC F | Lexus Team Petronas Tom's | 1:48.633 | 1:48.6330 | 1:51.7320 | 1:52.2560 | 1:50.4600 |
| 3rd | 17 | Tsukakoshi / Kaneishi | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:48.846 | 1:48.8460 | 1:51.7520 | 1:52.4120 | 1:49.9160 |
| 4th | 23 | Matsuda / Quintarelli | Nissan GT-R (R35) | NISMO | 1:48.863 | 1:48.8630 | 1:52.3740 | 1:51.8500 | 1:51.8500 |
| 5th | 18 | Yamamoto / Makowiecki | Honda NSX Concept-GT (NSX-P) | weider Modulo Dome Racing | 1:49.002 | 1:49.0020 | 1:52.7500 | 1:52.1280 | 1:49.9620 |
| 6th | 12 | Yasuda / de Oliveira | Nissan GT-R (R35) | Team Impul | 1:49.099 | 1:49.0990 | 1:52.6170 | 1:51.6400 | 1:50.4040 |
| 7th | 8 | Liuzzi / Matsuura | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:49.403 | 1:49.4030 | 1:52.4650 | 1:51.3740 | 1:49.8820 |
| 8th | 100 | Kogure / Mutou | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:49.449 | 1:49.4490 | 1:52.7520 | 1:54.4830 | 1:50.3780 |
| 9th | 1 | Tachikawa / Hirate | Lexus RC F | Lexus Team Zent Cerumo | 1:49.719 | 1:49.7190 | 1:53.9820 | 1:53.0610 | 1:51.7530 |
| 10th | 24 | Krumm / Sasaki | Nissan GT-R (R35) | Kondo Racing | 1:49.886 | 1:49.8860 | 1:52.9330 | 1:52.1640 | 1:50.0030 |
| 11th | 39 | Ishiura / Jarvis | Lexus RC F | Lexus Team Sard | 1:49.888 | 1:49.8880 | 1:52.6880 | 1:53.2410 | 1:50.3290 |
| 12th | 19 | Wakisaka / Sekiguchi | Lexus RC F | Lexus Team WedsSport Bandoh | 1:49.941 | 1:49.9410 | 1:53.1210 | 1:53.9760 | 1:50.9340 |
| 13th | 37 | Itou / Caldarelli | Lexus RC F | Lexus Team KeePer Tom's | 1:50.961 | 1:50.9610 | 1:54.4940 | 1:54.1000 | 1:51.9750 |
| 14th | 6 | Oshima / Kunimoto | Lexus RC F | Lexus Team Le Mans Eneos | 1:51.080 | 1:51.3220 | 1:54.2100 | 1:53.1090 | 1:51.0800 |
| 15th | 32 | Nakajima / Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:52.425 | no time | 1:53.4320 | 1:52.4250 | 1:52.4250 |
| 16th | 55 | Takagi / Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:59.115 | 1:59.1150 | 2:02.9490 | 2:04.0470 | 2:02.2080 |
| 17th | 0 | Nakayama / Nojiri / Michigami | Honda CR-Z (ZF2) | Team Mugen | 1:59.639 | 1:59.6390 | 2:02.8310 | 2:04.7780 | 2:04.7780 |
| 18th | 31 | Nitta / Saga / Nakayama | Toyota Prius (ZVW30) | Apr | 1:59.667 | 1:59.6670 | 2:02.8650 | 2:03.3230 | 2:01.8890 |
| 19th | 61 | Sasaki / Iguchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 2:00.034 | 2:00.0340 | 2:03.6590 | 2:01.9510 | 2:01.6410 |
| 20th | 3 | Hoshino / Ordoñez / Reip | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:00.398 | 2:00.3980 | 2:03.0520 | 2:03.2640 | 2:02.0470 |
| 21st | 60 | Iida / Yoshimoto / Satou | BMW Z4 GT3 (E89) | LM Corsa | 2:00.643 | 2:00.6430 | 2:02.7760 | 2:03.8800 | 2:02.4690 |
| 22nd | 10 | Ueda / Yamauchi | Mercedes-Benz SLS AMG GT3 | Gainer | 2:00.733 | 2:00.7330 | 2:03.0200 | 2:03.6080 | 2:01.9480 |
| 23rd | 360 | Tanaka / Yoshida / Fujita | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 2:00.898 | 2:00.8980 | 2:03.5610 | 2:02.0200 | 2:01.8250 |
| 24th | 65 | Kurosawa / Kurosawa | Mercedes-Benz SLS AMG GT3 | Leon Racing | 2:01.107 | 2:01.1070 | 2:03.8690 | 2:03.3530 | 2:01.8330 |
| 25th | 7 | Farfus / Ara / Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 2:01.196 | 2:01.1960 | 2:03.0710 | 2:03.3280 | 2:01.5810 |
| 26th | 9 | Shirasaka / Couto / Iida | Porsche 997 GT3 R | Pacific Direction Racing | 2:01.279 | 2:01.2790 | 2:03.6530 | 2:02.7120 | 2:02.0680 |
| 27th | 50 | Kano / Yasuoka / Indra-Payoong | Aston Martin V12 Vantage GT3 | Arnage Racing | 2:01.284 | 2:01.2840 | 2:04.0380 | 2:03.1970 | 2:02.7430 |
| 28th | 21 | Lyons / Fujii / Haase | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 2:01.293 | 2:01.2930 | 2:04.5130 | 2:02.7190 | 2:01.9140 |
| 29th | 22 | Wada / Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 2:01.320 | 2:01.3200 | 2:04.3470 | 2:04.4500 | 2:02.5410 |
| 30th | 48 | Takamori / Tanaka / Tomita | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:01.365 | 2:01.3650 | 2:04.2130 | 2:04.6030 | 2:02.1990 |
| 31st | 88 | Orido / Aoki / Hiramine | Lamborghini Gallardo GT3 (22-12226) | JLOC | 2:01.391 | 2:01.3910 | 2:04.0670 | 2:03.4950 | 2:02.0710 |
| 32nd | 4 | Taniguchi / Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 2:01.483 | 2:01.4830 | 2:03.9410 | 2:03.1270 | 2:02.7410 |
| 33rd | 11 | Hiranaka / Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 2:01.486 | 2:01.4860 | 2:04.2510 | 2:03.6900 | 2:02.1040 |
| 34th | 67 | Yokomizo / Mitsuyama / Mineo | Nissan GT-R Nismo GT3 (R35) | Team Taisan | 2:01.640 | 2:01.6400 | 2:04.5170 | 2:03.2160 | 2:03.2160 |
| 35th | 30 | Iwasaki / Kageyama / Azuma | Nissan GT-R Nismo GT3 (R35) | Apr | 2:01.714 | 2:01.7140 | 2:03.4320 | 2:03.1370 | 2:02.1930 |
| 36th | 33 | Tsuduki / Bergmeister / Bergmeister | Porsche 997 GT3 R | Porsche Team KTR | 2:01.728 | 2:01.7280 | 2:03.8550 | 2:04.7200 | 2:02.4330 |
| 37th | 5 | Tamanaka / Yamano / Tsuruta | Nissan GT-R Nismo GT3 (R35) | Team Mach | 2:01.797 | 2:01.7970 | 2:02.8450 | 2:03.2130 | 2:02.1230 |
| 38th | 2 | Takahashi / Katou / Hamaguchi | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 2:02.010 | no time | 2:04.1500 | 2:02.5270 | 2:02.0100 |
| 39th | 86 | Hosokawa / Yamanishi | Lamborghini Gallardo GT3 (09-7) | JLOC | 2:02.984 | 2:02.9840 | 2:04.1650 | 2:03.8340 | 2:03.0220 |