| 1st | 23 | Yanagida / Quintarelli | Nissan GT-R (R35) | Nismo | 1:52.1570 | 1:53.1010 | 1:52.1570 |
| 2nd | 18 | Yamamoto / Makowiecki | Honda HSV-010 GT (H010) | weider Modulo Dome Racing | 1:52.3590 | 1:52.6940 | 1:52.3590 |
| 3rd | 36 | Nakajima / Rossiter | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:52.4400 | 1:53.2310 | 1:52.4400 |
| 4th | 38 | Tachikawa / Hirate | Lexus SC430 (UZZ40) | Lexas Team Zent Cerumo | 1:52.5590 | 1:53.0580 | 1:52.5590 |
| 5th | 6 | Oshima / Kunimoto | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:52.6010 | 1:53.0400 | 1:52.6010 |
| 6th | 17 | Tsukakoshi / Kaneishi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:52.9930 | 1:53.5660 | 1:52.9930 |
| 7th | 37 | Itou / Caldarelli | Lexus SC430 (UZZ40) | Lexus Team KeePer Tom's | 1:53.2160 | 1:53.3990 | 1:53.2160 |
| 8th | 100 | Izawa / Kogure | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:53.2530 | 1:53.4020 | 1:53.2530 |
| 9th | 1 | Motoyama / Sekiguchi | Nissan GT-R (R35) | Mola | 1:53.7210 | 1:53.7210 | |
| 10th | 39 | Wakisaka / Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:53.7860 | 1:53.7860 | |
| 11th | 12 | Matsuda / de Oliveira | Nissan GT-R (R35) | Team Impul | 1:54.1050 | 1:54.1050 | |
| 12th | 19 | Ara / Couto | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:54.2500 | 1:54.2500 | |
| 13th | 24 | Yasuda / Krumm | Nissan GT-R (R35) | Kondo Racing | 1:54.2980 | 1:54.2980 | |
| 14th | 32 | Michigami / Nakajima | Honda HSV-010 GT (H010) | Nakajima Racing | 1:54.5530 | 1:54.5530 | |
| 15th | 8 | Firman / Matsuura | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:55.3690 | 1:55.3690 | |
| 17th | 61 | Yamano / Sasaki / Iguchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 2:01.4810 | 2:01.4810 | 2:01.6930 |
| 18th | 3 | Hoshino / Sasaki / Ordoñez | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:02.4750 | 2:02.8710 | 2:02.4750 |
| 19th | 50 | Kano / Yasuoka / Sakaguchi | Aston Martin V12 Vantage GT3 | Arnage Racing | 2:02.6800 | 2:03.3320 | 2:02.6800 |
| 20th | 33 | Kageyama / Fujii | Porsche 997 GT3 R | Hankook KTR | 2:03.1090 | 2:03.4830 | 2:03.1090 |
| 23rd | 52 | Takeuchi / Tsuchiya / Gamou | Mercedes-Benz SLS AMG GT3 | Okinawa-Imp Racing With Shift | 2:03.1210 | 2:03.1210 | 2:03.5690 |
| 24th | 55 | Takagi / Kobayashi / Nojiri | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 2:03.2290 | 2:03.2290 | 2:03.5730 |
| 21st | 62 | Kurosawa / Kurosawa / Nakaya | Mercedes-Benz SLS AMG GT3 | Leon Racing | 2:03.2670 | 2:03.8900 | 2:03.2670 |
| 22nd | 22 | Wada / Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 2:03.4950 | 2:03.9110 | 2:03.4950 |
| 27th | 0 | Mineo / Yokomizo | Porsche 997 GT3 R | Team Taisan Ken Endless | 2:03.6050 | 2:03.6050 | 2:04.0710 |
| 25th | 86 | Yamanishi / Hosokawa / Sakamoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 2:03.6300 | 2:03.6300 | 2:03.9200 |
| 28th | 21 | Tsuduki / Lyons | Audi R8 LMS | Hitotsuyama Racing | 2:03.7970 | 2:03.7970 | 2:04.9780 |
| 29th | 48 | Takamori / Chiyo / Tanaka | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:03.8070 | 2:03.8070 | 2:06.7830 |
| 26th | 9 | Mitsuyama / Yokomaku / Sakamoto | Porsche 997 GT3 R | Pacific Direction Racing | 2:03.9130 | 2:03.9130 | 2:04.0130 |
| 30th | 16 | Mutou / Nakayama | Honda CR-Z (ZF2) | Team Mugen | 2:03.9750 | 2:03.9750 | |
| 31st | 10 | Tanaka / Ueda / Kawaguchi | Mercedes-Benz SLS AMG GT3 | Gainer | 2:04.1710 | 2:04.1710 | |
| 32nd | 11 | Hiranaka / Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 2:04.1730 | 2:04.1730 | |
| 33rd | 4 | Taniguchi / Kataoka / Müller | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 2:04.1930 | 2:04.1930 | |
| 34th | 30 | Iwasaki / Sushko / Kobayashi | Audi R8 LMS Ultra (ABA-42BYHF) | Apr | 2:04.2160 | 2:04.2160 | |
| 35th | 31 | Nitta / Saga / Nakayama | Toyota Prius (ZVW30) | Apr | 2:04.2680 | 2:04.2680 | |
| 36th | 2 | Takahashi / Katou / van Dam | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 2:04.6260 | 2:04.6260 | |
| 37th | 88 | Orido / Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 2:05.4480 | 2:05.4480 | |
| 38th | 5 | Tamanaka / Yamashita / Omoto | Nissan GT-R Nismo GT3 (R35) | Team Mach | 2:06.6230 | 2:06.6230 | |
| 39th | 87 | Yamauchi / Yoshimoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 2:22.0330 | 2:22.0330 | |