| 1st | 46 | Motoyama / Yanagida | Nissan GT-R (R35) | Mola | 1:48.6290 | 1:48.6290 | 1:49.3530 |
| 2nd | 36 | Nakajima / Rossiter | Lexus RC F | Lexus Team Petronas Tom's | 1:48.6330 | 1:49.4010 | 1:48.6330 |
| 3rd | 17 | Tsukakoshi / Kaneishi | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:48.8460 | 1:49.5830 | 1:48.8460 |
| 4th | 23 | Matsuda / Quintarelli | Nissan GT-R (R35) | NISMO | 1:48.8630 | 1:48.8630 | 1:48.9790 |
| 5th | 18 | Yamamoto / Makowiecki | Honda NSX Concept-GT (NSX-P) | weider Modulo Dome Racing | 1:49.0020 | 1:49.0020 | 1:49.5710 |
| 6th | 12 | Yasuda / de Oliveira | Nissan GT-R (R35) | Team Impul | 1:49.0990 | 1:49.0990 | 1:49.4330 |
| 7th | 8 | Liuzzi / Matsuura | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:49.4030 | 1:49.4820 | 1:49.4030 |
| 8th | 100 | Kogure / Mutou | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:49.4490 | 1:49.4490 | 1:55.7080 |
| 9th | 1 | Tachikawa / Hirate | Lexus RC F | Lexus Team Zent Cerumo | 1:49.7190 | 1:49.7190 | |
| 10th | 24 | Krumm / Sasaki | Nissan GT-R (R35) | Kondo Racing | 1:49.8860 | 1:49.8860 | |
| 11th | 39 | Ishiura / Jarvis | Lexus RC F | Lexus Team Sard | 1:49.8880 | 1:49.8880 | |
| 12th | 19 | Wakisaka / Sekiguchi | Lexus RC F | Lexus Team WedsSport Bandoh | 1:49.9410 | 1:49.9410 | |
| 13th | 37 | Itou / Caldarelli | Lexus RC F | Lexus Team KeePer Tom's | 1:50.9610 | 1:50.9610 | |
| 14th | 6 | Oshima / Kunimoto | Lexus RC F | Lexus Team Le Mans Eneos | 1:51.3220 | 1:51.3220 | |
| 15th | 55 | Takagi / Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:59.1150 | 2:01.1450 | 1:59.1150 |
| 17th | 0 | Nakayama / Nojiri / Michigami | Honda CR-Z (ZF2) | Team Mugen | 1:59.6390 | 2:00.4240 | 1:59.6390 |
| 18th | 31 | Nitta / Saga / Nakayama | Toyota Prius (ZVW30) | Apr | 1:59.6670 | 2:00.4520 | 1:59.6670 |
| 19th | 61 | Sasaki / Iguchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 2:00.0340 | 2:00.2790 | 2:00.0340 |
| 20th | 3 | Hoshino / Ordoñez / Reip | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:00.3980 | 2:00.3980 | 2:00.4220 |
| 21st | 60 | Iida / Yoshimoto / Satou | BMW Z4 GT3 (E89) | LM Corsa | 2:00.6430 | 2:00.6430 | 2:00.9490 |
| 22nd | 10 | Ueda / Yamauchi | Mercedes-Benz SLS AMG GT3 | Gainer | 2:00.7330 | 2:00.7330 | 2:02.1440 |
| 23rd | 360 | Tanaka / Yoshida / Fujita | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 2:00.8980 | 2:00.8980 | no time |
| 24th | 65 | Kurosawa / Kurosawa | Mercedes-Benz SLS AMG GT3 | Leon Racing | 2:01.1070 | 2:01.1070 | 2:01.6680 |
| 25th | 7 | Farfus / Ara / Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 2:01.1960 | 2:01.1960 | 2:01.4150 |
| 26th | 9 | Shirasaka / Couto / Iida | Porsche 997 GT3 R | Pacific Direction Racing | 2:01.2790 | 2:01.2790 | 2:02.3640 |
| 27th | 50 | Kano / Yasuoka / Indra-Payoong | Aston Martin V12 Vantage GT3 | Arnage Racing | 2:01.2840 | 2:01.2840 | 2:02.3920 |
| 28th | 21 | Lyons / Fujii / Haase | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 2:01.2930 | 2:01.2930 | no time |
| 29th | 22 | Wada / Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 2:01.3200 | 2:01.3200 | |
| 30th | 48 | Takamori / Tanaka / Tomita | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:01.3650 | 2:01.3650 | |
| 31st | 88 | Orido / Aoki / Hiramine | Lamborghini Gallardo GT3 (22-12226) | JLOC | 2:01.3910 | 2:01.3910 | |
| 32nd | 4 | Taniguchi / Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 2:01.4830 | 2:01.4830 | |
| 33rd | 11 | Hiranaka / Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 2:01.4860 | 2:01.4860 | |
| 34th | 67 | Yokomizo / Mitsuyama / Mineo | Nissan GT-R Nismo GT3 (R35) | Team Taisan | 2:01.6400 | 2:01.6400 | |
| 35th | 30 | Iwasaki / Kageyama / Azuma | Nissan GT-R Nismo GT3 (R35) | Apr | 2:01.7140 | 2:01.7140 | |
| 36th | 33 | Tsuduki / Bergmeister / Bergmeister | Porsche 997 GT3 R | Porsche Team KTR | 2:01.7280 | 2:01.7280 | |
| 37th | 5 | Tamanaka / Yamano / Tsuruta | Nissan GT-R Nismo GT3 (R35) | Team Mach | 2:01.7970 | 2:01.7970 | |
| 38th | 86 | Hosokawa / Yamanishi | Lamborghini Gallardo GT3 (09-7) | JLOC | 2:02.9840 | 2:02.9840 | |
| 15th | 32 | Nakajima / Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | no time | no time | |
| 40th | 2 | Takahashi / Katou / Hamaguchi | McLaren MP4-12C GT3 | Cars Tokai Dream28 | no time | no time | |