| 1st | 6 | Juichi Wakisaka / Hideki Noda | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:24.3540 |
| 2nd | 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:24.4700 |
| 3rd | 30 | Hideki Okada / André Couto | McLaren F1 GTR (4S70) | Team Take One | 1:24.7790 |
| 4th | 36 | Takuya Kurosawa / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.1470 |
| 5th | 12 | Satoshi Motoyama / Naoki Hattori | Nissan Skyline GT-R (BNR34) | Team Impul | 1:25.2260 |
| 6th | 22 | Michael Krumm / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.4910 |
| 7th | 18 | Hiroki Katou / Sébastien Philippe | Honda NSX (GH-NA2) | Dome Mugen Project | 1:25.5050 |
| 8th | 21 | Akihiko Nakaya / Yasushi Hitotsuyama | McLaren F1 GTR (4S70) | Hitotsuyama Racing | 1:25.5290 |
| 9th | 39 | Masahiko Kageyama / Jeremie Dufour | Toyota Supra (JZA80) | Toyota Team SARD | 1:25.5380 |
| 10th | 100 | Akira Iida / Daisuke Itou | Honda NSX (GH-NA2) | Team Kunimitsu With Mooncraft | 1:25.6250 |
| 11th | 37 | Shin'ichi Yamaji / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.7280 |
| 12th | 25 | Manabu Orido / Seiji Ara | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:25.7790 |
| 13th | 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (GH-NA2) | Autobacs Racing Team Aguri | 1:25.9090 |
| 14th | 1 | Ryou Michigami / Hidetoshi Mitsusada | Honda NSX (GH-NA2) | Dome Mugen Project | 1:25.9240 |
| 15th | 33 | Ukyou Katayama / Masahiko Kondou | Toyota Supra (JZA80) | Toyota Team Cerumo With Cerumo | 1:26.0140 |
| 16th | 23 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:26.1190 |
| 17th | 64 | Tsugio Matsuda / Dominik Schwager | Honda NSX (GH-NA2) | Mobil1 Nakajima Racing | 1:26.1200 |
| 18th | 88 | Naohiro Furuya / Marco Apicella | Lamborghini Diablo (DE21) | JLOC | 1:31.5180 |
| 19th | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:33.0930 |
| 20th | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (GH-ZZW30) | ARTA With A'pex | 1:33.8400 |
| 21st | 7 | Haruhiko Matsumoto / Tetsuya Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:33.8690 |
| 22nd | 3 | Yuuji Ide / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 1:34.2940 |
| 23rd | 55 | Eiji Yamada / Takayuki Kinoshita | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 1:34.3700 |
| 24th | 26 | Hideo Fukuyama / Atsushi Yogou | Porsche 996 GT3-RS | Team Taisan Advan | 1:34.3720 |
| 25th | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D SPORT | 1:34.3860 |
| 26th | 910 | Hisashi Wada / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 1:34.4270 |
| 27th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 1:34.5710 |
| 28th | 62 | Shinsuke Shibahara / Yasuhisa Fujiwara | Porsche 996 GT3-R | R&D Sport | 1:34.6890 |
| 29th | 0 | Masahiro Matsunaga / Kumi Satou | Toyota MR-S (GH-ZZW30) | Tom's Spilit | 1:34.7720 |
| 30th | 900 | Dilantha Malagamuwa / Takeshi Asami | Mosler MT900R | Team Sri Lanka | 1:35.2490 |
| 31st | 360 | Kota Sasaki / Seigou Nishizawa | Ferrari 360 Modena (GFF360) | Dentaire Projet | 1:35.2750 |
| 32nd | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Racing Project Bandoh | 1:35.3380 |
| 33rd | 24 | Hideshi Matsuda / Kazuyuki Nishizawa | Porsche 996 GT3-R | Team Taisan Advan | 1:35.8130 |
| 34th | 11 | Jun'ichi Ikura / Yuusei Maki | Porsche 996 GT3-R | Team Gainer | 1:35.8850 |
| 35th | 51 | Naofumi Omoto / Yasukichi Yamamoto | Nissan Silvia (S15) | Auto Staff Racing Team | 1:36.2200 |
| 36th | 9 | Yukihiro Hane / Akira Watanabe | Porsche 996 GT3-R | Team Daikokuya | 1:36.2250 |
| 37th | 70 | Yoshimi Ishibashi / Hiroaki Suga | Porsche 996 GT3-RS | Team Gaikokuya | 1:36.6080 |
| 38th | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota Trueno (AE86) | Kraft | 1:36.7470 |
| 39th | 911 | Masamitsu Ishihara / Akira Hirakawa | Porsche 996 GT3-RS | 910 Racing | 1:37.4530 |
| 40th | 10 | Yutaka Yamagishi / Takahisa Oono | Porsche 993 RSR | Ability Motorsport | 1:43.5100 |