| 1st | 3 | Erik Comas / Toshihiro Kaneishi | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:14.1360 |
| 2nd | 12 | Benoit Tréluyer / Yuuji Ide | Nissan Fairlady Z (Z33) | Team Impul | 1:14.1900 |
| 3rd | 22 | Masami Kageyama / Michael Krumm | Nissan Fairlady Z (Z33) | NISMO | 1:14.2800 |
| 4th | 36 | Takeshi Tsuchiya / Marco Apicella | Toyota Supra (JZA80) | Toyota Team Tom's | 1:14.3470 |
| 5th | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:14.3980 |
| 6th | 37 | James Courtney / Tatsuya Kataoka | Toyota Supra (JZA80) | Toyota Team Tom's | 1:14.5620 |
| 7th | 18 | Ryou Michigami / Sébastien Philippe | Honda NSX (LA-NA2) | Dome Racing Team | 1:14.6520 |
| 8th | 38 | Yuuji Tachikawa / Seiji Ara | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:14.7450 |
| 9th | 32 | Tsugio Matsuda / Andre Lotterer | Honda NSX (LA-NA2) | Epson Nakajima Racing | 1:14.7540 |
| 10th | 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:14.8300 |
| 11th | 100 | Shinji Nakano / Hiroki Katou | Honda NSX (LA-NA2) | Team Kunimitsu With Moon Craft | 1:14.9100 |
| 12th | 8 | Katsutomo Kaneishi / Daisuke Itou | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:15.3240 |
| 13th | 39 | Jeremie Dufour / André Couto | Toyota Supra (JZA80) | Toyota Team SARD | 1:15.3290 |
| 14th | 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:15.3950 |
| 15th | 25 | Manabu Orido / Dominik Schwager | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:15.4690 |
| 16th | 15 | Genji Hashimoto / Norman Simon | Lamborghini Murcielago RG-1 (GH-BC10E) | Amprex Motorsports | 1:17.0410 |
| 17th | 21 | Hidetoshi Mitsusada / Tadao Uematsu | Ferrari 550 Maranello GTS | Hitotsuyama Racing | 1:18.2170 |
| 18th | 88 | Kouji Yamanishi / Hisashi Wada | Lamborghini Diablo (ZA90DE068) | JLOC | 1:19.1740 |
| 19th | 81 | Masataka Yanagida / Naofumi Omoto | Nissan Fairlady Z (Z33) | Team Daishin | 1:19.5880 |
| 20th | 63 | Hiroki Yoshimoto / "Osamu" | Vemac RD320R | Team LeyJun | 1:19.8900 |
| 21st | 80 | Mitsuhiro Kinoshita / Kazuki Hoshino | Nissan Fairlady Z (Z33) | Team Daishin | 1:19.9570 |
| 22nd | 31 | Minoru Tanaka / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | A'pex With Apr | 1:20.0690 |
| 23rd | 30 | Kota Sasaki / Satoshi Gotou | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:20.1720 |
| 24th | 11 | Hideshi Matsuda / Ichijou Suga | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:20.3880 |
| 25th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 1:20.3930 |
| 26th | 16 | Tetsuya Yamano / Hiroyuki Yagi | Honda NSX (LA-NA2) | M-Tec Co.Ltd. | 1:20.4850 |
| 27th | 10 | Tetsuya Tanaka / Atsushi Yogou | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:20.5200 |
| 28th | 19 | Takayuki Aoki / Nobuteru Taniguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:20.5300 |
| 29th | 52 | Hironori Takeuchi / Seigou Nishizawa | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:20.7920 |
| 30th | 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Vemac RD320R | Team Mach | 1:20.8860 |
| 31st | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:20.9430 |
| 32nd | 7 | Shin'ichi Yamaji / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:21.0980 |
| 33rd | 72 | Akira Hirakawa / Hideo Fukuyama | Porsche 996 GT3-RS | Team Gaikokuya | 1:21.2500 |
| 34th | 17 | Masahiro Matsunaga / Masaoki Nagashima | Toyota Celica (ZZT231) | Spirit Motorsport | 1:21.4420 |
| 35th | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:21.5360 |
| 36th | 9 | Gou Shimizu / Shin'ya Hosokawa | Mosler MT900R | A&S Racing | 1:21.6170 |
| 37th | 51 | Masanobu Katou / Katsuhiko Tsutsui | Nissan Silvia (S15) | Auto Staff Racing | 1:21.8050 |
| 38th | 20 | Yasuo Miyagawa / Takashi Inoue | Porsche 996 GT3-RSR | Hitotsuyama Racing | 1:22.0870 |
| 39th | 26 | Yutaka Yamagishi / Kaoru Ijiri | Porsche 996 GT3-RS | Team Taisan | 1:22.0980 |
| 40th | 111 | Hiroya Iijima / Takashi Ooi | Porsche 968 (E-968) | Arktech Motorsports | 1:22.1310 |
| 41st | 910 | Kazuyoshi Takamizawa / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 1:22.2160 |
| 42nd | 112 | Masaki Jounai / Akihiko Tsutsumi | Porsche 996 GT3-RS | Arktech Motorsports | 1:23.6760 |
| 43rd | 70 | Yoshimi Ishibashi / Isao Ihashi | Porsche 996 GT3-RS | Team Gaikokuya | 1:24.0250 |