| 1st | 12 | Yuuji Ide / Benoit Tréluyer | Nissan Fairlady Z (Z33) | Team Impul | 1:16.1000 |
| 2nd | 32 | Andre Lotterer / Tsugio Matsuda | Honda NSX (LA-NA2) | Nakajima Racing | 1:16.5600 |
| 3rd | 22 | Masataka Yanagida / Michael Krumm | Nissan Fairlady Z (Z33) | NISMO | 1:16.7070 |
| 4th | 100 | Sébastien Philippe / Jeremie Dufour | Honda NSX (LA-NA2) | Team Kunimitsu | 1:16.4430 |
| 5th | 3 | Toshihiro Kaneishi / Erik Comas | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:16.3590 |
| 6th | 6 | Akira Iida / Juichi Wakisaka | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:16.8050 |
| 7th | 38 | Toranosuke Takagi / Yuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:16.9830 |
| 8th | 36 | Takeshi Tsuchiya / James Courtney | Toyota Supra (JZA80) | Toyota Team Tom's | 1:16.9310 |
| 9th | 37 | Tatsuya Kataoka / Sakon Yamamoto | Toyota Supra (JZA80) | Toyota Team Tom's | 1:16.9160 |
| 10th | 39 | André Couto / Ronnie Quintarelli | Toyota Supra (JZA80) | Toyota Team SARD | 1:17.2700 |
| 11th | 18 | Ryō Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Honda Racing | 1:16.9820 |
| 12th | 8 | Ralph Firman / Daisuke Ito | Honda NSX (LA-NA2) | Team Honda Racing | 1:16.0990 |
| 13th | 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:17.0610 |
| 14th | 34 | Seiji Ara / Naoki Yokomizo | Toyota Supra (JZA80) | KRAFT | 1:17.0830 |
| 15th | 25 | Manabu Orido / Dominik Schwager | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:17.2410 |
| 16th | 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:17.7240 |
| 17th | 21 | Takuya Kurosawa / Hidetoshi Mitsusada | Ferrari 550 Maranello GTS | Hitotsuyama Racing | 1:18.8400 |
| 18th | 88 | Marco Apicella / Koji Yamanishi | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:21.1880 |
| 19th | 0 | Haruki Kurosawa / Shin'ya Hosokawa | Honda NSX (LA-NA2) | M-Tec Co.Ltd. | 1:23.9220 |
| 20th | 27 | Shogo Mitsuyama / Yasuo Miyagawa | Vemac RD320R | Direxiv Motorsports | 1:22.4640 |
| 21st | 62 | Tadao Uematsu / Shinsuke Shibahara | Vemac RD350R | Willcom R&D Sport | 1:23.4360 |
| 22nd | 7 | Shinichi Yamaji / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:23.4290 |
| 23rd | 13 | Masami Kageyama / Mitsuhiro Kinoshita | Nissan Fairlady Z (Z33) | Endless Sports | 1:23.7920 |
| 24th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 1:23.2230 |
| 25th | 46 | Kazuki Hoshino / Takayuki Aoki | Nissan Fairlady Z (Z33) | Mola | 1:23.7290 |
| 26th | 31 | Minoru Tanaka / Kazuki Nakajima | Toyota MR-S (GH-ZZW30) | Kicchouhouzan With Apr | 1:23.3770 |
| 27th | 30 | Tetsuya Yamano / Kota Sasaki | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:23.1180 |
| 28th | 77 | Tatsuya Tanigawa / Katsuo Kobayashi | Subaru Impreza (GDB) | Cusco Racing | 1:23.3770 |
| 29th | 19 | Nobuteru Taniguchi / Hiroki Kato | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:23.8550 |
| 30th | 11 | Tetsuya Tanaka / Paolo Montin | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:24.4070 |
| 31st | 10 | Yasutaka Hinoi / Hideshi Matsuda | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:23.9380 |
| 32nd | 2 | Kazuho Takahashi / Akira Watanabe | Vemac RD320R | Verno Tokai Dream28 | 1:24.3260 |
| 33rd | 9 | Eiji Yamada / Jun'ichirou Yamashita | Mosler MT900R | A&S Racing | 1:24.8270 |
| 34th | 87 | Hisashi Wada / Naohiro Furuya | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:24.9220 |
| 35th | 777 | Tomohiko Sunako / Kazuyoshi Takamizawa | Porsche 996 GT3-RS | 910 Racing | 1:24.9720 |
| 36th | 72 | Akihiko Asai / Akira Hirakawa | Porsche 996 GT3-RSR | Teramoto Technical Office | 1:25.1150 |
| 37th | 47 | Gou Shimizu / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Mola | 1:25.1830 |
| 38th | 110 | Ichijou Suga / Takashi Ooi | Porsche 986 Boxster | Arktech Motorsports | 1:26.0080 |
| 39th | 111 | Masaki Jounai / Hiroya Iijima | Porsche 968 (E-968) | Team LeyJun | 1:26.6010 |
| 40th | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 1:26.9370 |
| 41st | 70 | Yoshimi Ishibashi / Hirofumi Takei | Porsche 996 GT3-RS | Team Gaikokuya | 1:27.3820 |
| 42nd | 52 | Hironori Takeuchi / Katsuyuki Hiranaka | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:27.5550 |
| 43rd | 913 | Hideo Fukuyama / Syougo Suhou | Chevrolet Corvette C6 (GH-X245) | A&S Racing | 1:28.8140 |