| 1st | 22 | Michael Krumm / Masataka Yanagida | Nissan GT-R | Nismo | 1:52.1650 |
| 2nd | 23 | Benoit Tréluyer / Satoshi Motoyama | Nissan GT-R | Nismo | 1:51.5420 |
| 3rd | 12 | Sébastien Philippe / Tsugio Matsuda | Nissan GT-R | Team Impul | 1:52.3780 |
| 4th | 36 | Andre Lotterer / Juichi Wakisaka | Lexus SC430 (UZZ40) | Petronas Toyota Team Tom's | 1:52.7050 |
| 5th | 38 | Yuuji Tachikawa / Richard Lyons | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:53.0000 |
| 6th | 18 | Takashi Kogure / Ryou Michigami | Honda NSX (LA-NA2) | Dome Racing Team | 1:52.8600 |
| 7th | 32 | Loïc Duval / Katsuyuki Hiranaka | Honda NSX (LA-NA2) | Nakajima Racing | 1:53.0790 |
| 8th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan GT-R | Kondo Racing | 1:52.9630 |
| 9th | 100 | Yuuji Ide / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:53.6110 |
| 10th | 1 | Ralph Firman / Takuya Izawa | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:53.1160 |
| 11th | 3 | Naoki Yokomizo / Ronnie Quintarelli | Nissan GT-R | Hasemi Motorsport | 1:53.7470 |
| 12th | 17 | Toshihiro Kaneishi / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Real Racing With Leon | 1:53.7830 |
| 13th | 6 | Daisuke Itou / Björn Wirdheim | Lexus SC430 (UZZ40) | Eneos Toyota Team Le Mans | 1:54.1040 |
| 14th | 25 | Takeshi Tsuchiya / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:54.1430 |
| 15th | 35 | Tatsuya Kataoka / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:54.2840 |
| 16th | 39 | André Couto / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:54.8730 |
| 17th | 2 | Hiroki Katou / Kazuho Takahashi | Shiden MC/RT-16 | Cars Tokai Dream28 | 2:05.2110 |
| 18th | 7 | Hiroyuki Iiri / Ryou Orime | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:06.3490 |
| 19th | 26 | Nobuteru Taniguchi / Shin'ichi Yamaji | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 2:06.3680 |
| 20th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 2:06.4670 |
| 21st | 46 | Kazuki Hoshino / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 2:07.0670 |
| 22nd | 81 | Takayuki Aoki / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Team Daishin | 2:06.4490 |
| 23rd | 19 | Manabu Orido / Tsubasa Abe | Toyota Celica (ZZT231) | Racing Project Bandoh | 2:07.3760 |
| 24th | 77 | Tetsuya Yamano / Kota Sasaki | Subaru Impreza (GD) | Cusco Racing | 2:07.1840 |
| 25th | 110 | Daisuke Ikeda / Hidetoshi Mitsusada | Porsche 986 Boxster | Arktech Motorsports | 2:07.4040 |
| 26th | 66 | Atsushi Yogou / Kouji Yamanishi | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 2:06.4890 |
| 27th | 95 | Kouhei Hirate / Keisuke Kunimoto | Toyota MR-S (GH-ZZW30) | Apr | 2:07.4180 |
| 28th | 11 | Masayuki Ueda / Tetsuya Tanaka | Ferrari F430 (GF-F360) | Jim Gainer | 2:07.4290 |
| 29th | 4 | Ryohei Sakaguchi / Masaki Matsushita | Vemac RD320R | Team Uematsu Nova | 2:07.9820 |
| 30th | 31 | Yuuya Sakamoto / Kyousuke Mineo | Toyota MR-S (GH-ZZW30) | Apr | 2:08.2170 |
| 31st | 5 | Tetsuji Tamanaka / Naoya Yamano | Vemac RD320R | Team Mach | 2:08.6430 |
| 32nd | 111 | Masaki Jounai / Hiroshi Koizumi | Porsche 986 Boxster | Arktech Motorsports | 2:08.7440 |
| 33rd | 33 | Mitsuhiro Kinoshita / Masami Kageyama | Porsche 997 GT3 RSR | Hankook KTR | 2:09.1090 |
| 34th | 16 | Tadao Uematsu / Katsuhiko Tsutsui | Vemac RD350R | Team Uematsu Nova | 2:09.8590 |
| 35th | 70 | Yutaka Yamagishi / Takehide Maeda | Porsche 996 GT3-RS | Team Gaikokuya | 2:10.2430 |
| 36th | 118 | Takashi Ooi / Takshi Miyamoto | Porsche 996 GT3-RS | Tomei Sports | 2:10.4700 |
| 37th | 666 | Syougo Suhou / Jun'ichirou Yamashita | Vemac RD320R | Avanzza Rosso | 2:10.6400 |
| 38th | 27 | Takashi Inoue / Hwang Jin-Woo | Porsche 996 GT3-RSR | Team Shadow | 2:11.0130 |
| 39th | 62 | Shinsuke Shibahara / Haruki Kurosawa | Vemac RD408R | Willcom R&D Sport | 2:20.5230 |
| 40th | 87 | Hisashi Wada / Muneyuki Kurihara | Lamborghini Gallardo RG-3 | JLOC | no time |
| 41st | 88 | Hideshi Matsuda / Naohiro Furuya | Lamborghini Gallardo RG-3 | JLOC | no time |