| 1st | 46 | Satoshi Motoyama / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:47.7490 |
| 2nd | 38 | Yuuji Tachikawa / Hiroaki Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:47.9410 |
| 3rd | 64 | Daisuke Nakajima / Bertrand Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:48.0220 |
| 4th | 15 | Takashi Kogure / Oliver Turvey | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:48.1170 |
| 5th | 17 | Koudai Tsukakoshi / Hideki Mutou | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:48.1490 |
| 6th | 37 | Andrea Caldarelli / Ryō Hirakawa | Lexus RC F (USC10) | Lexus Team KeePer Tom's | 1:48.2580 |
| 7th | 1 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | NISMO | 1:48.3940 |
| 8th | 12 | Hironobu Yasuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:48.5670 |
| 9th | 36 | Daisuke Itou / James Rossiter | Lexus RC F (USC10) | Lexus Team Petronas Tom's | 1:48.5690 |
| 10th | 19 | Juichi Wakisaka / Yuuhi Sekiguchi | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:48.7580 |
| 11th | 39 | Kouhei Hirate / Heikki Kovalainen / Christian Klien | Lexus RC F (USC10) | Lexus Team Sard | 1:48.9840 |
| 12th | 8 | Kousuke Matsuura / Tomoki Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:49.0140 |
| 13th | 24 | Daiki Sasaki / Michael Krumm | Nissan GT-R (R35) | Kondo Racing | 1:49.0670 |
| 14th | 100 | Naoki Yamamoto / Takuya Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:50.0750 |
| 15th | 31 | Kouki Saga / Yuichi Nakayama / Kota Sasaki | Toyota Prius (ZVW30) | Apr | 1:59.0770 |
| 16th | 61 | Takuto Iguchi / Hideki Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:59.2400 |
| 17th | 360 | Hiroki Yoshida / Atsushi Tanaka / Masato Narisawa | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:59.2990 |
| 18th | 88 | Manabu Orido / Kazuki Hiramine / Kimiya Satou | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:59.3160 |
| 19th | 18 | Yuuki Nakayama / Marko Asmer / Nick Cassidy | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:59.3990 |
| 20th | 25 | Takeshi Tsuchiya / Takamitsu Matsui / Tatsuya Tanigawa | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:59.5070 |
| 21st | 21 | Richard Lyons / Tomonobu Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:59.5140 |
| 22nd | 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:59.8260 |
| 23rd | 10 | André Couto / Katsumasa Chiyo / Ryuichiro Tomita | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:59.8390 |
| 24th | 55 | Shinichi Takagi / Takashi Kobayashi / Nirei Hukuzumi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:59.9060 |
| 25th | 2 | Kazuho Takahashi / Hiroki Katou / Hiroshi Hamaguchi | Lotus Evora MC (122) | Cars Tokai Dream28 | 1:59.9610 |
| 26th | 5 | Tetsuji Tamanaka / Shogo Mitsuyama | Toyota 86 MC (86/ZN6) | Team Mach | 2:00.1480 |
| 27th | 7 | Seiji Ara / Jörg Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 2:00.1950 |
| 28th | 77 | Naoki Yokomizo / Kyousuke Mineo / Taiyo Iida | Ferrari 458 Italia GT3 | Direction Racing | 2:00.2310 |
| 29th | 33 | Yuuya Sakamoto / Kenta Yamashita | Porsche 997 GT3 R | Porsche Team KTR | 2:00.2740 |
| 30th | 3 | Kazuki Hoshino / Mitsunori Takaboshi / Wolfgang Reip | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:00.2960 |
| 31st | 0 | Nobuteru Taniguchi / Tatsuya Kataoka | Mercedes-Benz SLS AMG GT3 | Goodsmile Racing & TeamUkyo | 2:00.4120 |
| 32nd | 51 | Morio Nitta / Shigekazu Wakisaka | BMW Z4 GT3 (E89) | LM Corsa | 2:00.4510 |
| 33rd | 65 | Haruki Kurosawa / Naoya Gamou | Mercedes-Benz SLS AMG GT3 (197) | Leon Racing | 2:00.4660 |
| 34th | 50 | Masaki Kano / Nanin Indra-Payoong / Hideto Yasuoka | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 2:01.0320 |
| 35th | 48 | Hiroshi Takamori / Masaki Tanaka / Yuusaku Shibata | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:01.1100 |
| 36th | 30 | Hiroshi Koizumi / Yuuki Iwasaki | Nissan GT-R Nismo GT3 (R35) | Apr | 2:01.2120 |
| 37th | 60 | Akira Iida / Hiroki Yoshimoto / Dominik Farnbacher | Lexus RC F GT3 (USC10) | LM Corsa | 2:01.3570 |
| 38th | 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motor Sports | 2:01.4360 |
| 39th | 111 | Masayuki Ueda / Kazuya Tsuruta / Shin Ikegami | Mercedes-Benz SLS AMG GT3 | Rn-sports | 2:01.5880 |
| 40th | 9 | Takuya Shirasaka / Ryohei Sakaguchi / Daisuke Yamawaki | McLaren MP4-12C GT3 | Pacific Racing | 2:01.8570 |
| 41st | 87 | Takayuki Aoki / Kouji Yamanishi / Yoshitaka Kuroda | Lamborghini Gallardo GT-3 (09-7) | JLOC | 2:02.0770 |