| 1st | 12 | Yasuda / de Oliveira | Nissan GT-R (R35) | Team Impul | 1:28.799 | 1:28.7990 | 1:30.4980 | 1:30.8410 | 1:30.4840 |
| 2nd | 46 | Motoyama / Yanagida | Nissan GT-R (R35) | Mola | 1:29.272 | 1:29.2720 | 1:31.0240 | 1:31.8080 | 1:29.9540 |
| 3rd | 23 | Matsuda / Quintarelli | Nissan GT-R (R35) | NISMO | 1:29.380 | 1:29.3800 | 1:30.5800 | 1:30.5370 | 1:29.8360 |
| 4th | 36 | Rossiter / Hirakawa | Lexus RC F | Lexus Team Petronas Tom's | 1:29.510 | 1:29.5100 | 1:31.0880 | 1:31.6890 | 1:29.9370 |
| 5th | 1 | Tachikawa / Hirate | Lexus RC F | Lexus Team Zent Cerumo | 1:29.525 | 1:29.5250 | 1:31.5310 | 1:31.7130 | 1:30.5360 |
| 6th | 24 | Krumm / Sasaki | Nissan GT-R (R35) | Kondo Racing | 1:29.558 | 1:29.5580 | 1:31.4770 | 1:31.9340 | 1:29.6820 |
| 7th | 39 | Ishiura / Jarvis | Lexus RC F | Lexus Team Sard | 1:29.824 | 1:29.8240 | 1:31.4900 | 1:32.0120 | 1:30.6550 |
| 8th | 37 | Itou / Caldarelli | Lexus RC F | Lexus Team KeePer Tom's | 1:29.987 | 1:29.9870 | 1:31.3670 | 1:31.8540 | 1:30.7190 |
| 9th | 19 | Wakisaka / Sekiguchi | Lexus RC F | Lexus Team WedsSport Bandoh | 1:30.399 | 1:30.3990 | 1:31.9720 | 1:32.1330 | 1:31.0160 |
| 10th | 6 | Oshima / Kunimoto | Lexus RC F | Lexus Team Le Mans Eneos | 1:30.650 | 1:30.6500 | 1:31.8340 | 1:31.7180 | 1:31.0690 |
| 11th | 18 | Yamamoto / Vernay | Honda NSX Concept-GT (NSX-P) | weider Modulo Dome Racing | 1:30.986 | 1:30.9860 | 1:32.7690 | 1:32.7230 | 1:32.5480 |
| 12th | 17 | Tsukakoshi / Kaneishi | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:31.061 | 1:31.0610 | 1:55.8130 | 1:33.4860 | 1:31.4500 |
| 13th | 100 | Kogure / Mutou | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:31.419 | 1:31.4190 | 1:32.8550 | 1:33.0990 | 1:31.9340 |
| 14th | 32 | Nakajima / Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:31.882 | 1:31.9690 | 1:33.5530 | 1:33.3910 | 1:31.8820 |
| 15th | 8 | Liuzzi / Matsuura | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:32.086 | 1:32.4770 | 1:33.0910 | 1:34.6280 | 1:32.0860 |
| 16th | 3 | Hoshino / Ordoñez | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:37.841 | 1:37.8410 | 1:39.8700 | 1:39.3800 | 1:38.8350 |
| 17th | 61 | Sasaki / Iguchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:38.034 | 1:38.0340 | 1:39.7370 | 1:39.6470 | 1:39.3190 |
| 18th | 55 | Takagi / Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:38.078 | 1:38.0780 | 1:40.0880 | 1:39.8160 | 1:39.4730 |
| 19th | 2 | Takahashi / Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:38.109 | 1:38.1090 | 1:39.3370 | 1:38.9290 | 1:38.9060 |
| 20th | 30 | Iwasaki / Kageyama | Nissan GT-R Nismo GT3 (R35) | Apr | 1:38.204 | 1:38.2040 | 1:40.1010 | 1:40.0350 | 1:40.0820 |
| 21st | 0 | Nakayama / Nojiri | Honda CR-Z (ZF2) | Team Mugen | 1:38.320 | 1:38.3200 | 1:39.6610 | 1:40.0190 | 1:40.4280 |
| 22nd | 7 | Ara / Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:38.408 | 1:38.4080 | 1:39.9340 | 1:39.0370 | 1:39.4670 |
| 23rd | 31 | Nitta / Saga | Toyota Prius (ZVW30) | Apr | 1:38.533 | 1:38.5330 | 1:39.5050 | 1:38.8430 | 1:39.7880 |
| 24th | 9 | Shirasaka / Sakamoto / Iida | Porsche 997 GT3 R | Pacific Direction Racing | 1:38.595 | 1:38.5950 | 1:39.9220 | 1:39.3460 | 1:38.9010 |
| 25th | 86 | Hosokawa / Yamanishi | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:38.635 | 1:38.6350 | 1:40.2030 | 1:39.9550 | 1:39.7950 |
| 26th | 4 | Taniguchi / Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:38.778 | 1:38.7780 | 1:39.7980 | 1:39.1040 | 1:38.9050 |
| 27th | 11 | Hiranaka / Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:39.017 | 1:39.0170 | 1:39.5520 | 1:40.2670 | 1:39.3430 |
| 28th | 360 | Tanaka / Yoshida / Fujita | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:39.071 | 1:39.0710 | 1:40.2660 | 1:39.5300 | 1:39.3770 |
| 29th | 67 | Yokomizo / Mitsuyama | Nissan GT-R Nismo GT3 (R35) | Team Taisan | 1:39.255 | 1:39.6530 | 1:39.7330 | 1:39.2550 | 1:39.3110 |
| 30th | 88 | Orido / Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:39.273 | 1:39.2730 | 1:41.4450 | 1:39.8640 | 1:40.2750 |
| 31st | 10 | Ueda / Yamauchi | Mercedes-Benz SLS AMG GT3 | Gainer | 1:39.459 | 1:39.4590 | 1:39.9180 | 1:40.8730 | 1:40.0270 |
| 32nd | 65 | Kurosawa / Mineo / Kurosawa | Mercedes-Benz SLS AMG GT3 | Leon Racing | 1:39.483 | 1:39.8500 | 1:40.3080 | 1:39.7490 | 1:39.4830 |
| 33rd | 60 | Iida / Yoshimoto | BMW Z4 GT3 (E89) | LM Corsa | 1:39.555 | 1:39.5550 | 1:39.6880 | 1:40.0390 | 1:40.2500 |
| 34th | 5 | Tamanaka / Yamashita / Tsuruta | Nissan GT-R Nismo GT3 (R35) | Team Mach | 1:39.611 | 1:39.6110 | 1:40.9160 | 1:40.2400 | 1:40.3110 |
| 35th | 50 | Kano / Yasuoka / Indra-Payoong | Aston Martin V12 Vantage GT3 | Arnage Racing | 1:39.692 | 1:39.6920 | 1:40.7890 | 1:40.0310 | 1:40.1970 |
| 36th | 22 | Wada / Tsuchiya | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 1:39.766 | 1:39.7660 | 1:40.9000 | 1:40.6830 | 1:40.7460 |
| 37th | 33 | Tsuduki / Bergmeister | Porsche 997 GT3 R | Porsche Team KTR | 1:39.807 | 1:44.0590 | 1:40.3320 | 1:39.8070 | 1:40.1520 |
| 38th | 21 | Fujii / van Dam | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:39.826 | 1:39.8260 | 1:40.5410 | 1:40.5120 | 1:40.2960 |
| 39th | 48 | Takamori / Tanaka / Inoue | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:41.383 | no time | | | 1:41.3830 |