| 1st | 64 | Ralph Firman / Tsugio Matsuda | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:59.2910 |
| 2nd | 36 | Takeshi Tsuchiya / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:59.3280 |
| 3rd | 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:59.8330 |
| 4th | 18 | Sébastien Philippe / Richard Lyons | Honda NSX (LA-NA2) | Dome Mugen Project | 2:00.1710 |
| 5th | 37 | Takuya Kurosawa / Paolo Montin | Toyota Supra (JZA80) | Toyota Team Tom's | 2:00.2090 |
| 6th | 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 2:00.4400 |
| 7th | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 2:00.6370 |
| 8th | 22 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 2:00.6480 |
| 9th | 16 | Dominik Schwager / Daisuke Itou | Honda NSX (LA-NA2) | Dome Mugen Project | 2:01.0310 |
| 10th | 76 | Naoki Hattori / Eiichi Tajima | McLaren F1 GTR (19R GTR) | Hitotsuyama Racing | 2:01.1190 |
| 11th | 23 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 2:01.2840 |
| 12th | 12 | Tetsuya Tanaka / Kazuyoshi Hoshino | Nissan Skyline GT-R (BNR34) | Team Impul | 2:01.3920 |
| 13th | 33 | Masahiko Kondou / Hayanari Shimoda | Toyota Supra (JZA80) | Toyota Team Cerumo | 2:01.6170 |
| 14th | 39 | Jeremie Dufour / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 2:02.4360 |
| 15th | 35 | Masahiko Kageyama / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 2:03.2130 |
| 16th | 25 | Shin'ichi Yamaji / Seiji Ara | Toyota Supra (JZA80) | Tsuchiya Engineering | 2:03.2660 |
| 17th | 88 | Marco Apicella / Hisashi Wada | Lamborghini Diablo JGT-1 (ZA90DE068) | JLOC | 2:05.6470 |
| 18th | 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 2:09.8210 |
| 19th | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (ZZW30) | Racing Project Bandoh | 2:10.2140 |
| 20th | 7 | Haruhiko Matsumoto / Nobuteru Taniguchi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:10.2950 |
| 21st | 3 | Tetsuya Yamano / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 2:10.5070 |
| 22nd | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 2:10.8310 |
| 23rd | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (ZZW30) | ARTA With A'pex | 2:11.1470 |
| 24th | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (ZZW30) | KRAFT | 2:11.5510 |
| 25th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 2:11.6390 |
| 26th | 55 | Eiji Yamada / Takayuki Kinoshita | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 2:11.8830 |
| 27th | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 2:12.3760 |
| 28th | 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 2:12.3890 |
| 29th | 24 | Hideo Fukuyama / Mitsuhiro Kinoshita | Porsche 996 GT3-R | Team Taisan Advan | 2:12.4820 |
| 30th | 910 | Hideshi Matsuda / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 2:12.5840 |
| 31st | 26 | Atsushi Yogou / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 2:13.6730 |
| 32nd | 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 2:13.6800 |
| 33rd | 9 | Yousuke Shimojima / Masanobu Takenaka | Porsche 996 GT3-R | Team Daikokuya | 2:14.3050 |
| 34th | 28 | Yukihiro Hane / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan Jr. | 2:14.6740 |
| 35th | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 2:15.8630 |
| 36th | 21 | Yasushi Hitotsuyama / Yasushi Kikuchi | BMW M3 GT (E46) | Hitotsuyama Racing | 2:16.8720 |
| 37th | 70 | Yoshimi Ishibashi / Patrick van Schoote | Porsche 996 GT3-RS | Team Gaikokuya | 2:17.3890 |