| 1st | 38 | Yuuji Tachikawa / Seiji Ara | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:43.7250 |
| 2nd | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:44.0310 |
| 3rd | 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:44.1050 |
| 4th | 37 | James Courtney / Tatsuya Kataoka | Toyota Supra (JZA80) | Toyota Team Tom's | 1:44.4850 |
| 5th | 22 | Masami Kageyama / Michael Krumm | Nissan Fairlady Z (Z33) | NISMO | 1:44.5160 |
| 6th | 39 | Jeremie Dufour / André Couto | Toyota Supra (JZA80) | Toyota Team SARD | 1:44.5780 |
| 7th | 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:44.8130 |
| 8th | 25 | Manabu Orido / Dominik Schwager | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:45.5950 |
| 9th | 3 | Toshihiro Kaneishi / Erik Comas | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:45.8560 |
| 10th | 8 | Katsutomo Kaneishi / Daisuke Itou | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:45.9740 |
| 11th | 32 | Tsugio Matsuda / Andre Lotterer | Honda NSX (LA-NA2) | Epson Nakajima Racing | 1:46.1960 |
| 12th | 18 | Ryou Michigami / Sébastien Philippe | Honda NSX (LA-NA2) | Dome Racing Team | 1:46.2420 |
| 13th | 36 | Takeshi Tsuchiya / Marco Apicella | Toyota Supra (JZA80) | Toyota Team Tom's | 1:46.6160 |
| 14th | 12 | Benoit Tréluyer / Yuuji Ide | Nissan Fairlady Z (Z33) | Team Impul | 1:48.4520 |
| 15th | 21 | Hidetoshi Mitsusada / Tadao Uematsu | Ferrari 550 Maranello GTS | Hitotsuyama Racing | 1:49.0310 |
| 16th | 80 | Mitsuhiro Kinoshita / Kazuki Hoshino | Nissan Fairlady Z (Z33) | Team Daishin | 1:50.6010 |
| 17th | 10 | Tetsuya Tanaka / Atsushi Yogou | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:50.8490 |
| 18th | 30 | Kota Sasaki / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:50.9830 |
| 19th | 19 | Takayuki Aoki / Nobuteru Taniguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:51.1670 |
| 20th | 7 | Shin'ichi Yamaji / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:51.1870 |
| 21st | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 1:51.4720 |
| 22nd | 16 | Tetsuya Yamano / Hiroyuki Yagi | Honda NSX (LA-NA2) | M-Tec Co.Ltd. | 1:51.5460 |
| 23rd | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:51.7330 |
| 24th | 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Vemac RD320R | Team Mach | 1:52.0080 |
| 25th | 81 | Masataka Yanagida / Naofumi Omoto | Nissan Fairlady Z (Z33) | Team Daishin | 1:52.0900 |
| 26th | 11 | Hideshi Matsuda / Ichijou Suga | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:52.1050 |
| 27th | 52 | Hironori Takeuchi / Seigou Nishizawa | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:52.1400 |
| 28th | 31 | Minoru Tanaka / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | A'pex With Apr | 1:52.1670 |
| 29th | 88 | Kouji Yamanishi / Hisashi Wada | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:52.2670 |
| 30th | 17 | Masahiro Matsunaga / Masaoki Nagashima | Toyota Celica (ZZT231) | Spirit Motorsport | 1:52.9750 |
| 31st | 72 | Akira Hirakawa / Hideo Fukuyama | Porsche 996 GT3-RS | Team Gaikokuya | 1:53.7120 |
| 32nd | 26 | Yutaka Yamagishi / Kaoru Ijiri | Porsche 996 GT3-RS | Team Taisan | 1:53.8730 |
| 33rd | 63 | "Osamu" / Takaya Tsubobayashi | Vemac RD320R | Team LeyJun | 1:53.9390 |
| 34th | 9 | Gou Shimizu / Shin'ya Hosokawa | Mosler MT900R | A&S Racing | 1:54.1020 |
| 35th | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:55.0500 |
| 36th | 910 | Kazuyoshi Takamizawa / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 1:55.2180 |
| 37th | 100 | Shinji Nakano / Hiroki Katou | Honda NSX (LA-NA2) | Team Kunimitsu With Moon Craft | 1:55.2710 |
| 38th | 51 | Masanobu Katou / Katsuhiko Tsutsui | Nissan Silvia (S15) | Auto Staff Racing | 1:55.5130 |
| 39th | 20 | Hiroshi Wada / Takashi Inoue | Porsche 996 GT3-RSR | Hitotsuyama Racing | 1:55.6020 |
| 40th | 70 | Yoshimi Ishibashi / Hiromi Kozono | Porsche 996 GT3-RS | Team Gaikokuya | 1:58.8320 |