| 1st | 8 | Ralph Firman / Daisuke Itou | Honda NSX (LA-NA2) | Team Honda Racing | 1:46.1030 |
| 2nd | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Honda Racing | 1:46.1950 |
| 3rd | 100 | Sébastien Philippe / Jeremie Dufour | Honda NSX (LA-NA2) | Team Kunimitsu | 1:46.1110 |
| 4th | 38 | Toranosuke Takagi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:46.3050 |
| 5th | 3 | Toshihiro Kaneishi / Erik Comas | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:46.2010 |
| 6th | 12 | Benoit Tréluyer / Yuuji Ide | Nissan Fairlady Z (Z33) | Team Impul | 1:46.5390 |
| 7th | 22 | Masataka Yanagida / Michael Krumm | Nissan Fairlady Z (Z33) | NISMO | 1:46.2630 |
| 8th | 32 | Andre Lotterer / Tsugio Matsuda | Honda NSX (LA-NA2) | Nakajima Racing | 1:46.4630 |
| 9th | 6 | Akira Iida / Juichi Wakisaka | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:46.2370 |
| 10th | 34 | Naoki Yokomizo / Seiji Ara | Toyota Supra (JZA80) | KRAFT | 1:46.4670 |
| 11th | 37 | Tatsuya Kataoka / Sakon Yamamoto | Toyota Supra (JZA80) | Toyota Team Tom's | 1:46.5580 |
| 12th | 25 | Manabu Orido / Dominik Schwager | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:46.6150 |
| 13th | 39 | André Couto / Ronnie Quintarelli | Toyota Supra (JZA80) | Toyota Team SARD | 1:46.6270 |
| 14th | 36 | Takeshi Tsuchiya / James Courtney | Toyota Supra (JZA80) | Toyota Team Tom's | 1:46.7850 |
| 15th | 35 | Peter Dumbreck / Naoki Hattori | Toyota Supra (JZA80) | KRAFT | 1:46.8550 |
| 16th | 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:47.3300 |
| 17th | 21 | Hidetoshi Mitsusada / Takuya Kurosawa | Ferrari 550 Maranello GTS | Hitotsuyama Racing | 1:47.8300 |
| 18th | 88 | Marco Apicella / Kouji Yamanishi | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:51.4920 |
| 19th | 46 | Kazuki Hoshino / Takayuki Aoki | Nissan Fairlady Z (Z33) | Mola | 1:54.1050 |
| 20th | 19 | Nobuteru Taniguchi / Hiroki Katou | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:55.6830 |
| 21st | 7 | Shin'ichi Yamaji / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:55.4280 |
| 22nd | 2 | Akira Watanabe / Kazuho Takahashi | Vemac RD320R | Verno Tokai Dream28 | 1:55.2790 |
| 23rd | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 1:55.0520 |
| 24th | 77 | Tatsuya Tanigawa / Katsuo Kobayashi | Subaru Impreza (GDB) | Cusco Racing | 1:55.6400 |
| 25th | 30 | Kota Sasaki / Tetsuya Yamano | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:55.4630 |
| 26th | 27 | Yasuo Miyagawa / Shogo Mitsuyama | Vemac RD320R | Direxiv Motorsports | 1:55.2890 |
| 27th | 10 | Yasutaka Hinoi / Hideshi Matsuda | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:55.7920 |
| 28th | 87 | Naohiro Furuya / Hisashi Wada | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:55.8950 |
| 29th | 31 | Minoru Tanaka / Kazuki Nakajima | Toyota MR-S (GH-ZZW30) | Kicchouhouzan With Apr | 1:55.9140 |
| 30th | 11 | Tetsuya Tanaka / Paolo Montin | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:55.9190 |
| 31st | 13 | Mitsuhiro Kinoshita / Masami Kageyama | Nissan Fairlady Z (Z33) | Endless Sports | 1:56.0180 |
| 32nd | 62 | Tadao Uematsu / Shinsuke Shibahara | Vemac RD350R | Willcom R&D Sport | 1:56.1110 |
| 33rd | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 1:56.3710 |
| 34th | 47 | Gou Shimizu / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Mola | 1:56.4310 |
| 35th | 52 | Hironori Takeuchi / Katsuyuki Hiranaka | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:56.5600 |
| 36th | 0 | Haruki Kurosawa / Shin'ya Hosokawa | Honda NSX (LA-NA2) | M-Tec Co.Ltd. | 1:56.6400 |
| 37th | 777 | Tomohiko Sunako / Kazuyoshi Takamizawa | Porsche 996 GT3-RS | 910 Racing | 1:56.7670 |
| 38th | 112 | Atsushi Yogou / Takaya Tsubobayashi | Porsche 996 GT3 (GF99663) | Arktech Motorsports | 1:58.4660 |
| 39th | 72 | Akira Hirakawa / Takashi Inoue | Porsche 996 GT3-RSR | Teramoto Technical Office | 1:59.5770 |
| 40th | 70 | Yoshimi Ishibashi / Hirofumi Takei | Porsche 996 GT3-RS | Team Gaikokuya | 1:59.5840 |
| 41st | 111 | Hiroya Iijima / Masaki Jounai | Porsche 968 (E-968) | Team LeyJun | 1:59.8610 |
| 42nd | 110 | Ichijou Suga / Takashi Ooi | Porsche 986 Boxster | Arktech Motorsports | 2:00.4080 |
| 43rd | 9 | Syougo Suhou / Jun'ichirou Yamashita | Mosler MT900R | A&S Racing | 2:01.8060 |
| 44th | 913 | Hideo Fukuyama / Eiji Yamada | Chevrolet Corvette C6 (GH-X245) | A&S Racing | 2:05.6570 |