| 1st | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:24.3030 |
| 2nd | 1 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:24.3860 |
| 3rd | 76 | Naoki Hattori / Eiichi Tajima | McLaren F1 GTR (19R GTR) | Hitotsuyama Racing | 1:24.4230 |
| 4th | 36 | Takeshi Tsuchiya / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:24.7040 |
| 5th | 30 | Hideki Okada / Haruki Kurosawa | McLaren F1 GTR (19R GTR) | Team Take One | 1:24.7260 |
| 6th | 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:24.8870 |
| 7th | 39 | Jeremie Dufour / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:24.9800 |
| 8th | 64 | Ralph Firman / Tsugio Matsuda | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:25.0110 |
| 9th | 16 | Dominik Schwager / Daisuke Itou | Honda NSX (LA-NA2) | Dome Mugen Project | 1:25.0130 |
| 10th | 37 | Takuya Kurosawa / Paolo Montin | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.0710 |
| 11th | 100 | Hidetoshi Mitsusada / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:25.1180 |
| 12th | 18 | Sébastien Philippe / Richard Lyons | Honda NSX (LA-NA2) | Dome Mugen Project | 1:25.2110 |
| 13th | 12 | Tetsuya Tanaka / Kazuyoshi Hoshino | Nissan Skyline GT-R (BNR34) | Team Impul | 1:25.2570 |
| 14th | 22 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.3430 |
| 15th | 35 | Masahiko Kageyama / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:25.3930 |
| 16th | 23 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.5260 |
| 17th | 25 | Shin'ichi Yamaji / Geoff Lees | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:25.6550 |
| 18th | 88 | Marco Apicella / Hisashi Wada | Lamborghini Diablo JGT-1 (ZA90DE068) | JLOC | 1:28.4750 |
| 19th | 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 1:32.3790 |
| 20th | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:32.5210 |
| 21st | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (ZZW30) | Racing Project Bandoh | 1:32.6620 |
| 22nd | 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 1:33.0440 |
| 23rd | 71 | Masaki Jounai / Keita Sawa | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:33.0530 |
| 24th | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (ZZW30) | ARTA With A'pex | 1:33.0950 |
| 25th | 24 | Hideo Fukuyama / Mitsuhiro Kinoshita | Porsche 996 GT3-R | Team Taisan Advan | 1:33.1170 |
| 26th | 55 | Eiji Yamada / Gou Shimizu | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 1:33.1330 |
| 27th | 910 | Hideshi Matsuda / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 1:33.1390 |
| 28th | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (ZZW30) | KRAFT | 1:33.2050 |
| 29th | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:33.3380 |
| 30th | 3 | Tetsuya Yamano / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 1:33.3810 |
| 31st | 26 | Takayuki Kinoshita / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 1:33.5800 |
| 32nd | 7 | Haruhiko Matsumoto / Nobuteru Taniguchi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:33.6910 |
| 33rd | 17 | Masahiro Matsunaga / Takeshi Namekawa | Toyota MR-S (ZZW30) | Tom's Spirit | 1:34.1570 |
| 34th | 360 | Seigou Nishizawa / Kota Sasaki | Ferrari 360 Modena (GF-F360) | Dentaire Projet Racing | 1:34.3480 |
| 35th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 1:34.4110 |
| 36th | 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 1:34.6170 |
| 37th | 28 | Tomohiko Sunako / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan Jr. | 1:34.7950 |
| 38th | 9 | Yousuke Shimojima / Masanobu Takenaka | Porsche 996 GT3-R | Team Daikokuya | 1:35.1920 |
| 39th | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 1:35.2950 |
| 40th | 61 | Tsubasa Kurosawa / Yasuo Miyagawa | Porsche 996 GT3-RS | R&D Sport Ex | 1:35.3420 |
| 41st | 21 | Yasushi Hitotsuyama / Yasushi Kikuchi | BMW M3 GT (E46) | Hitotsuyama Racing | 1:35.4020 |
| 42nd | 911 | Akira Hirakawa / Shigemitsu Haga | Porsche 996 GT3-RS | 910 Racing | 1:35.5090 |
| 43rd | 70 | Yoshimi Ishibashi / Patrick van Schoote | Porsche 996 GT3-RS | Team Gaikokuya | 1:37.0300 |
| 44th | 4 | Toshiyuki Yamamoto / Izumi Yoshida | Chevrolet Corvette (C-4) | Zipspeed | 1:48.1460 |