| 1st | 1 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | NISMO | 1:28.0220 |
| 2nd | 12 | Hironobu Yasuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:28.1480 |
| 3rd | 36 | Daisuke Itou / James Rossiter | Lexus RC F (USC10) | Lexus Team Petronas Tom's | 1:28.6800 |
| 4th | 17 | Koudai Tsukakoshi / Hideki Mutou | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:28.7690 |
| 5th | 38 | Yuuji Tachikawa / Hiroaki Ishiura | Lexus RC F (USC10) | Lexus Team Zent Cerumo | 1:28.8450 |
| 6th | 24 | Daiki Sasaki / Lucas Ordoñez | Nissan GT-R (R35) | Kondo Racing | 1:28.8490 |
| 7th | 39 | Kouhei Hirate / Heikki Kovalainen | Lexus RC F (USC10) | Lexus Team Sard | 1:28.8820 |
| 8th | 15 | Takashi Kogure / Oliver Turvey | Honda NSX Concept-GT (NSX-P) | Drago Modulo Honda Racing | 1:28.9210 |
| 9th | 46 | Satoshi Motoyama / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:28.9730 |
| 10th | 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus RC F (USC10) | Lexus Team Le Mans Eneos | 1:29.0500 |
| 11th | 100 | Naoki Yamamoto / Takuya Izawa | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:29.1640 |
| 12th | 64 | Daisuke Nakajima / Bertrand Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:29.3010 |
| 13th | 8 | Kousuke Matsuura / Tomoki Nojiri | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:29.5430 |
| 14th | 37 | Andrea Caldarelli / Ryo Hirakawa | Lexus RC F (USC10) | Lexus Team KeePer Tom's | 1:29.5840 |
| 15th | 19 | Juichi Wakisaka / Yuuhi Sekiguchi | Lexus RC F (USC10) | Lexus Team WedsSport Bandoh | 1:29.6160 |
| 16th | 31 | Kota Sasaki / Yuichi Nakayama / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:36.5190 |
| 17th | 65 | Haruki Kurosawa / Naoya Gamou | Mercedes-Benz SLS AMG GT3 (197) | Leon Racing | 1:37.5580 |
| 18th | 3 | Kazuki Hoshino / Mitsunori Takaboshi | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:37.7200 |
| 19th | 25 | Takeshi Tsuchiya / Takamitsu Matsui | Toyota 86 MC (MC86) | Vivac Team Tsuchiya | 1:37.7530 |
| 20th | 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:37.7960 |
| 21st | 0 | Nobuteru Taniguchi / Tatsuya Kataoka | Mercedes-Benz SLS AMG GT3 | Goodsmile Racing & TeamUkyo | 1:37.8700 |
| 22nd | 10 | André Couto / Katsumasa Chiyo / Ryuichiro Tomita | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:37.9230 |
| 23rd | 61 | Takuto Iguchi / Hideki Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:38.1730 |
| 24th | 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:38.1830 |
| 25th | 88 | Manabu Orido / Kazuki Hiramine / Kimiya Satou | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:38.1950 |
| 26th | 7 | Seiji Ara / Jörg Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:38.2020 |
| 27th | 360 | Hiroki Yoshida / Atsushi Tanaka / Masato Narisawa | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:38.2780 |
| 28th | 21 | Richard Lyons / Tomonobu Fujii / Stéphane Ortelli | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:38.3490 |
| 29th | 33 | Alexandre Imperatori / Kenta Yamashita | Porsche 997 GT3 R | Porsche Team KTR | 1:38.3790 |
| 30th | 18 | Yuuki Nakayama / Marko Asmer / Yuuji Ide | Toyota 86 MC (86/ZN6) | Team Upgarage With Bandoh | 1:38.4670 |
| 31st | 77 | Naoki Yokomizo / Kyousuke Mineo / Taiyo Iida | Ferrari 458 Italia GT3 | Direction Racing | 1:38.7680 |
| 32nd | 30 | Hiroshi Koizumi / Yuuki Iwasaki / Masami Kageyama | Nissan GT-R Nismo GT3 (R35) | Apr | 1:38.7700 |
| 33rd | 51 | Morio Nitta / Shigekazu Wakisaka | BMW Z4 GT3 (E89) | LM Corsa | 1:38.7910 |
| 34th | 9 | Takuya Shirasaka / Tohjiro Azuma / Daisuke Yamawaki | McLaren MP4-12C GT3 | Pacific Racing | 1:39.2950 |
| 35th | 5 | Tetsuji Tamanaka / Shogo Mitsuyama / Jun'ichirou Yamashita | Toyota 86 MC (86/ZN6) | Team Mach | 1:39.3050 |
| 36th | 48 | Hiroshi Takamori / Masaki Tanaka / Yuusaku Shibata | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:39.3620 |
| 37th | 50 | Masaki Kano / Nanin Indra-Payoong / Hideto Yasuoka | Mercedes-Benz SLS AMG GT3 (197) | Arnage Racing | 1:39.4360 |
| 38th | 87 | Takayuki Aoki / Kouji Yamanishi | Lamborghini Gallardo GT-3 (09-7) | JLOC | 1:39.4580 |
| 39th | 111 | Masayuki Ueda / Kazuya Tsuruta / Shin Ikegami | Mercedes-Benz SLS AMG GT3 | Rn-sports | 1:39.6670 |
| 40th | 60 | Akira Iida / Hiroki Yoshimoto | Lexus RC F GT3 (USC10) | LM Corsa | 1:40.1350 |
| 41st | 86 | Chris Mamerow / Shin'ya Hosokawa / Yoshitaka Kuroda | Audi R8 LMS Ultra | Audi Team Racing Tech | 1:40.8830 |