| 1st | 64 | Tom Coronel / Hidetoshi Mitsusada | Honda NSX (E-NA2) | Mobil1 Nakajima Racing | 1:43.2350 |
| 2nd | 16 | Osamu Nakako / Ryou Michigami | Honda NSX (E-NA2) | Mugen & Dome Project | 1:43.5730 |
| 3rd | 18 | Juichi Wakisaka / Katsutomo Kaneishi | Honda NSX (E-NA2) | Mugen & Dome Project | 1:43.5920 |
| 4th | 6 | Hideki Noda / Wayne Gardner | Toyota Supra (JZA80) | Esso Tiger Team Le Mans | 1:44.2680 |
| 5th | 100 | Kunimitsu Takahashi / Akira Iida | Honda NSX (E-NA2) | Team Kunimitsu with Moncraft | 1:44.3430 |
| 6th | 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:44.4030 |
| 7th | 36 | Masanori Sekiya / Takuya Kurosawa | Toyota Supra (JZA80) | Toyota Castrol Team TOM'S | 1:44.5610 |
| 8th | 32 | Takayuki Kinoshita / Masahiko Kondo | Toyota Supra (JZA80) | cdma One Toyota Team Cerumo with Key's | 1:44.7550 |
| 9th | 1 | Erik Comas / Satoshi Motoyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:45.0360 |
| 10th | 30 | Youji Yamada / Hideki Okada | McLaren F1 GTR (S70) | Team Take One | 1:45.2960 |
| 11th | 39 | Keiichi Tsuchiya / Masahiko Kageyama | Toyota Supra (JZA80) | Toyota Team SARD | 1:45.5610 |
| 12th | 2 | Aguri Suzuki / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:45.6930 |
| 13th | 3 | Masahiro Hasemi / Tetsuya Tanaka | Nissan Skyline GT-R (BCNR33) | Hasemi Motorsports | 1:45.7310 |
| 14th | 12 | Kazuyoshi Hoshino / Masami Kageyama | Nissan Skyline GT-R (BNR34) | Team Impul | 1:45.9530 |
| 15th | 37 | Toshio Suzuki / Ukyo Katayama | Toyota Supra (JZA80) | Toyota Castrol Team TOM'S | 1:46.7350 |
| 16th | 55 | Eiichi Tajima / Yasuyuki Honjo | Chrysler Viper GTS | Team Taisan with Advan | 1:49.2090 |
| 17th | 19 | Manabu Orido / Takahiko Hara | Toyota Celica (ST205) | Racing Project Bandoh | 1:53.3580 |
| 18th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GC4) | Cusco Racing | 1:53.5470 |
| 19th | 7 | Haruhiko Matsumoto / Tetsuya Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:53.6230 |
| 20th | 25 | Morio Nitta / Shinichi Takagi | Toyota MR-2 (SW20) | Momocorse Racing Team with Tsuchiya | 1:53.6250 |
| 21st | 15 | Takeshi Tsuchiya / Yuuji Ide | Nissan Silvia (S15) | NISMO | 1:54.0750 |
| 22nd | 81 | Hideo Fukuyama / Nobuyuki Ohyagi | Nissan Silvia (S15) | Team Daishin | 1:54.1020 |
| 23rd | 72 | Akira Ishikawa / Kou Hirano | Mazda RX-7 (FD3S) | Okura Rotary Racing | 1:57.6620 |
| 24th | 88 | Hisashi Wada / Naohiro Furuya | Lamborghini Diablo (ZA90DE068) | JLOC | 1:55.5530 |
| 25th | 26 | Hideshi Matsuda / Dominik Schwager | Porsche 996 GT3-R | Team Taisan Jr. with Advan | no time |