| 1st | 3 | Ronnie Quintarelli / Naoki Yokomizo | Nissan GT-R | Hasemi Motorsport | 1:45.1280 |
| 2nd | 1 | Ralph Firman / Takuya Izawa | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:45.6430 |
| 3rd | 35 | Tatsuya Kataoka / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:45.8890 |
| 4th | 22 | Michael Krumm / Masataka Yanagida | Nissan GT-R | Nismo | 1:45.9360 |
| 5th | 39 | André Couto / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:45.9380 |
| 6th | 36 | Andre Lotterer / Juichi Wakisaka | Lexus SC430 (UZZ40) | Petronas Toyota Team Tom's | 1:46.2580 |
| 7th | 23 | Benoit Tréluyer / Satoshi Motoyama | Nissan GT-R | Nismo | 1:46.2980 |
| 8th | 12 | Tsugio Matsuda / Sébastien Philippe | Nissan GT-R | Team Impul | 1:46.3460 |
| 9th | 6 | Akira Iida / Björn Wirdheim | Lexus SC430 (UZZ40) | Eneos Toyota Team Le Mans | 1:46.4270 |
| 10th | 100 | Yuuji Ide / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:46.4740 |
| 11th | 38 | Yuuji Tachikawa / Richard Lyons | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:46.5220 |
| 12th | 18 | Takashi Kogure / Ryou Michigami | Honda NSX (LA-NA2) | Dome Racing Team | 1:46.6150 |
| 13th | 32 | Katsuyuki Hiranaka / Loic Duval | Honda NSX (LA-NA2) | Nakajima Racing | 1:46.9490 |
| 14th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan GT-R | Kondo Racing | 1:47.7460 |
| 15th | 25 | Takeshi Tsuchiya / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:48.1950 |
| 16th | 17 | Toshihiro Kaneishi / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Real Racing With Leon | 1:51.2980 |
| 17th | 110 | Hidetoshi Mitsusada / Daisuke Ikeda | Porsche 986 Boxster | Arktech Motorsports | 1:55.7100 |
| 18th | 33 | Masami Kageyama / Mitsuhiro Kinoshita | Porsche 997 GT3 RSR | Hankook KTR | 1:56.3040 |
| 19th | 66 | Kouji Yamanishi / Atsushi Yogou | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:56.4660 |
| 20th | 26 | Nobuteru Taniguchi / Shin'ichi Yamaji | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 1:56.4960 |
| 21st | 4 | Masaki Matsushita / Ryohei Sakaguchi | Vemac RD320R | Team Uematsu Nova | 1:56.6440 |
| 22nd | 62 | Haruki Kurosawa / Shinsuke Shibahara | Vemac RD408R | Willcom R&D Sport | 1:56.6490 |
| 23rd | 52 | Takuya Kurosawa / Takuto Iguchi | Lexus IS350 (GSE21) | Team Takeuchi With Shift | 1:56.7190 |
| 24th | 2 | Hiroki Katou / Kazuho Takahashi | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:57.0420 |
| 25th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:57.0970 |
| 26th | 11 | Tetsuya Tanaka / Masayuki Ueda | Ferrari F430 (GF-F360) | Jim Gainer | 1:57.1240 |
| 27th | 77 | Kota Sasaki / Tetsuya Yamano | Subaru Impreza (GD) | Cusco Racing | 1:57.2650 |
| 28th | 7 | Hiroyuki Iiri / Ryou Orime | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:57.3710 |
| 29th | 111 | Tsubasa Kurosawa / Hiroshi Koizumi | Porsche 986 Boxster | Arktech Motorsports | 1:57.4060 |
| 30th | 46 | Kazuki Hoshino / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 1:57.4320 |
| 31st | 5 | Tetsuji Tamanaka / Naoya Yamano | Vemac RD320R | Team Mach | 1:57.6950 |
| 32nd | 81 | Takayuki Aoki / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Team Daishin | 1:57.7680 |
| 33rd | 87 | Muneyuki Kurihara / Hisashi Wada | Lamborghini Gallardo RG-3 | JLOC | 1:57.8020 |
| 34th | 88 | Hideshi Matsuda / Naohiro Furuya | Lamborghini Gallardo RG-3 | JLOC | 1:57.8820 |
| 35th | 95 | Hideki Yamauchi / Keisuke Kunimoto | Toyota MR-S (GH-ZZW30) | Apr | 1:58.2160 |
| 36th | 118 | Masayuki Kurihara / Takshi Miyamoto | Porsche 996 GT3-RS | Tomei Sports | 1:58.2820 |
| 37th | 70 | Yutaka Yamagishi / Yoshimi Ishibashi | Porsche 996 GT3-RS | Team Gaikokuya | 1:58.3890 |
| 38th | 27 | Takashi Inoue / Hwang Jin-Woo | Porsche 996 GT3-RSR | Team Shadow | 1:58.8650 |
| 39th | 31 | Yuuya Sakamoto / Kyousuke Mineo | Toyota MR-S (GH-ZZW30) | Apr | 1:59.2140 |
| 40th | 666 | Jun'ichirou Yamashita / Syougo Suhou | Vemac RD320R | Avanzza Rosso | 2:00.0080 |