| 1st | 64 | Daisuke Nakajima / Bertrand Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:47.7400 |
| 2nd | 38 | Yuuji Tachikawa / Hiroaki Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:48.0410 |
| 3rd | 36 | Daisuke Itou / James Rossiter | Lexus RC F (USC10) | Lexus Team Petronas Tom's | 1:48.3490 |
| 4th | 39 | Kouhei Hirate / Heikki Kovalainen | Lexus RC F (USC10) | Lexus Team Sard | 1:48.4320 |
| 5th | 37 | Andrea Caldarelli / Ryō Hirakawa | Lexus RC F (USC10) | Lexus Team KeePer Tom's | 1:48.5010 |
| 6th | 12 | Hironobu Yasuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:48.6510 |
| 7th | 100 | Naoki Yamamoto / Takuya Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:48.6550 |
| 8th | 19 | Juichi Wakisaka / Yuuhi Sekiguchi | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:48.6910 |
| 9th | 17 | Koudai Tsukakoshi / Hideki Mutou | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:49.4160 |
| 10th | 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus RC F (USC10) | Lexus Team Le Mans Eneos | 1:49.5330 |
| 11th | 24 | Daiki Sasaki / Michael Krumm | Nissan GT-R (R35) | Kondo Racing | 1:49.6160 |
| 12th | 1 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | NISMO | 1:49.7570 |
| 13th | 46 | Satoshi Motoyama / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:49.7610 |
| 14th | 8 | Kousuke Matsuura / Tomoki Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:49.9840 |
| 15th | 15 | Takashi Kogure / Oliver Turvey | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:51.0970 |
| 16th | 31 | Kouki Saga / Yuichi Nakayama | Toyota Prius (ZVW30) | Apr | 1:56.2230 |
| 17th | 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:56.9050 |
| 18th | 10 | André Couto / Katsumasa Chiyo | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:57.4690 |
| 19th | 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:57.8530 |
| 20th | 88 | Manabu Orido / Kazuki Hiramine | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:57.9740 |
| 21st | 0 | Nobuteru Taniguchi / Tatsuya Kataoka | Mercedes-Benz SLS AMG GT3 | Goodsmile Racing & TeamUkyo | 1:58.1930 |
| 22nd | 61 | Takuto Iguchi / Hideki Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:58.2710 |
| 23rd | 5 | Tetsuji Tamanaka / Shogo Mitsuyama | Toyota 86 MC (86/ZN6) | Team Mach | 1:58.5000 |
| 24th | 77 | Naoki Yokomizo / Kyousuke Mineo | Ferrari 458 Italia GT3 | Direction Racing | 1:58.6560 |
| 25th | 21 | Richard Lyons / Tomonobu Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:58.7210 |
| 26th | 25 | Takeshi Tsuchiya / Tatsuya Tanigawa | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:58.8950 |
| 27th | 65 | Haruki Kurosawa / Naoya Gamou | Mercedes-Benz SLS AMG GT3 (197) | Leon Racing | 1:59.0410 |
| 28th | 33 | Yuuya Sakamoto / Kenta Yamashita | Porsche 997 GT3 R | Porsche Team KTR | 1:59.2050 |
| 29th | 7 | Seiji Ara / Jörg Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:59.2390 |
| 30th | 3 | Kazuki Hoshino / Mitsunori Takaboshi | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:59.3480 |
| 31st | 20 | Yuuki Nakayama / Yuuji Ide | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:59.5420 |
| 32nd | 87 | Takayuki Aoki / Kimiya Satou | Lamborghini Gallardo GT-3 (09-7) | JLOC | 1:59.5770 |
| 33rd | 51 | Morio Nitta / Shigekazu Wakisaka | BMW Z4 GT3 (E89) | LM Corsa | 1:59.8940 |
| 34th | 360 | Hiroki Yoshida / Atsushi Tanaka | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 2:00.6990 |
| 35th | 60 | Akira Iida / Hiroki Yoshimoto | Lexus RC F GT3 (USC10) | LM Corsa | 2:00.9540 |
| 36th | 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motor Sports | 2:01.0370 |
| 37th | 50 | Masaki Kano / Nanin Indra-Payoong | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 2:01.1350 |
| 38th | 48 | Hiroshi Takamori / Masaki Tanaka | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:01.1540 |
| 39th | 111 | Masayuki Ueda / Kazuya Tsuruta | Mercedes-Benz SLS AMG GT3 | Rn-sports | 2:01.2350 |
| 40th | 47 | Keiichi Inoue / Yuusaku Shibata | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:02.2470 |
| 41st | 9 | Takuya Shirasaka / Ryohei Sakaguchi | McLaren MP4-12C GT3 | Pacific Racing | 2:02.3270 |
| 42nd | 2 | Kazuho Takahashi / Hiroki Katou | Lotus Evora MC (122) | Cars Tokai Dream28 | 2:02.6740 |
| 43rd | 30 | Hiroshi Koizumi / Yuuki Iwasaki | Nissan GT-R Nismo GT3 (R35) | Apr | 2:02.7240 |