| 1st | 32 | Loic Duval / Hideki Mutou | Honda NSX (LA-NA2) | Epson Nakajima Racing | 1:33.1080 |
| 2nd | 35 | Naoki Hattori / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:33.9230 |
| 3rd | 3 | Naoki Yokomizo / Joao Paolo de Oliveira | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:34.2140 |
| 4th | 24 | Masataka Yanagida / Seiji Ara | Nissan Fairlady Z (Z33) | Kondo Racing | 1:34.3370 |
| 5th | 1 | Yuuji Tachikawa / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:34.3630 |
| 6th | 8 | Daisuke Itou / Ralph Firman | Honda NSX (LA-NA2) | Team Honda Racing | 1:34.3540 |
| 7th | 36 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:34.6930 |
| 8th | 6 | Akira Iida / Tatsuya Kataoka | Lexus SC430 (UZZ40) | Mobil1 Toyota Team Le Mans | 1:34.4830 |
| 9th | 22 | Michael Krumm / Sakon Yamamoto | Nissan Fairlady Z (Z33) | Nismo | 1:34.6610 |
| 10th | 25 | Manabu Orido / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Team Tsuchiya | 1:34.6680 |
| 11th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Honda Racing | 1:34.7870 |
| 12th | 23 | Satoshi Motoyama / Tsugio Matsuda | Nissan Fairlady Z (Z33) | Nismo | 1:35.1360 |
| 13th | 100 | Sébastien Philippe / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:35.2350 |
| 14th | 66 | André Couto / Katsuyuki Hiranaka | Toyota Supra (JZA80) | Toyota Team Sard | 1:35.2970 |
| 15th | 12 | Benoit Tréluyer / Kazuki Hoshino | Nissan Fairlady Z (Z33) | Team Impul | 1:35.6780 |
| 17th | 777 | Kazuya Oshima / Minoru Tanaka | Toyota MR-S (GH-ZZW30) | Ryouzanpaku With Apr | 1:42.3120 |
| 18th | 19 | Kouji Matsuda / Shigekazu Wakisaka | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:42.6470 |
| 19th | 9 | Osamu Nakajima / Masaki Tanaka | Mosler MT900R | A&S Racing | 1:42.6790 |
| 20th | 96 | Takuya Kurosawa / Tsubasa Kurosawa | Vemac RD350R | Ebbro Team Nova | 1:42.4890 |
| 21st | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 1:42.9420 |
| 22nd | 62 | Shinsuke Shibahara / Hiroyuki Yagi | Vemac RD408R | Willcom R&D Sport | 1:42.8230 |
| 23rd | 46 | Kota Sasaki / Taku Bamba | Nissan Fairlady Z (Z33) | Mola | 1:42.7550 |
| 24th | 47 | Masaoki Nagashima / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 1:42.8870 |
| 25th | 110 | Hideshi Matsuda / Ichijou Suga | Porsche 986 Boxster | Arktech Motorsports | 1:42.8960 |
| 26th | 26 | Shin'ichi Yamaji / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 1:42.9560 |
| 27th | 7 | Tetsuya Yamano / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:42.9590 |
| 28th | 101 | Morio Nitta / Shinichi Takagi | Toyota MR-S (GH-ZZW30) | Apr | 1:42.9600 |
| 29th | 2 | Kazuho Takahashi / Hiroki Katou | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:43.0090 |
| 30th | 11 | Tetsuya Tanaka / Takayuki Aoki | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:43.0880 |
| 31st | 55 | Hidetoshi Mitsusada / Daisuke Ikeda | Ford GT (DHG-replica) | Dhg Racing | 1:43.5780 |
| 32nd | 88 | Marco Apicella / Yasutaka Hinoi | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:43.5850 |
| 33rd | 14 | Mitsuhiro Kinoshita / Kyousuke Mineo | Porsche 996 GT3-RS | Endless Sports | 1:43.5960 |
| 34th | 910 | Tadao Uematsu / Ryohei Sakaguchi | Porsche 996 GT3-RSR | 910 Racing With Team Ishimatsu | 1:43.6190 |
| 35th | 87 | Kouji Yamanishi / Hisashi Wada | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:43.8050 |
| 36th | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 1:43.8710 |
| 37th | 61 | Shogo Mitsuyama / Nobuteru Taniguchi | Vemac RD320R | R&D Sport | 1:43.9070 |
| 38th | 77 | Katsuo Kobayashi / Yasushi Kikuchi | Subaru Impreza (GD) | Cusco Racing | 1:44.2120 |
| 39th | 10 | Hiromi Kozono / Naofumi Omoto | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:44.2120 |
| 40th | 52 | Hironori Takeuchi / Kouki Saga | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:44.4840 |
| 41st | 111 | Hiroya Iijima / Masaki Jounai | Porsche 996 GT3 Cup | Team LeyJun | 1:44.9300 |
| 42nd | 666 | Syougo Suhou / Jun'ichirou Yamashita | Honda NSX (GH-NA2) | Team Bomex Dream28 | 1:45.4060 |
| 43rd | 170 | Yoshimi Ishibashi / Kazuyoshi Takamizawa | Porsche 996 GT3-RS | Team Gaikokuya | 1:47.6240 |