| 1st | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Honda Racing | 1:41.0290 |
| 2nd | 8 | Daisuke Itou / Ralph Firman | Honda NSX (LA-NA2) | Team Honda Racing | 1:41.2090 |
| 3rd | 23 | Tsugio Matsuda / Satoshi Motoyama | Nissan Fairlady Z (Z33) | Nismo | 1:40.8670 |
| 4th | 100 | Sébastien Philippe / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:41.2570 |
| 5th | 12 | Benoit Tréluyer / Kazuki Hoshino | Nissan Fairlady Z (Z33) | Team Impul | 1:42.2640 |
| 6th | 1 | Yuuji Tachikawa / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:42.0980 |
| 7th | 22 | Michael Krumm / Richard Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:41.8880 |
| 8th | 25 | Manabu Orido / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Team Tsuchiya | 1:42.1050 |
| 9th | 6 | Akira Iida / Tatsuya Kataoka | Lexus SC430 (UZZ40) | Mobil1 Toyota Team Le Mans | 1:41.8820 |
| 10th | 66 | André Couto / Katsuyuki Hiranaka | Toyota Supra (JZA80) | Toyota Team Sard | 1:42.0830 |
| 11th | 36 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:43.0150 |
| 12th | 35 | Naoki Hattori / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:43.0600 |
| 13th | 24 | Masataka Yanagida / Seiji Ara | Nissan Fairlady Z (Z33) | Kondo Racing | 1:43.2880 |
| 14th | 3 | Naoki Yokomizo / Joao Paolo de Oliveira | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:44.3310 |
| 15th | 32 | Loic Duval / Hideki Mutou | Honda NSX (LA-NA2) | Epson Nakajima Racing | 1:45.1600 |
| 17th | 2 | Hiroki Katou / Kazuho Takahashi | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:50.4750 |
| 18th | 96 | Takuya Kurosawa / Tsubasa Kurosawa | Vemac RD350R | Ebbro Team Nova | 1:50.1990 |
| 19th | 7 | Tetsuya Yamano / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:50.5110 |
| 20th | 101 | Morio Nitta / Shinichi Takagi | Toyota MR-S (GH-ZZW30) | Apr | 1:51.1530 |
| 21st | 777 | Minoru Tanaka / Kazuya Oshima | Toyota MR-S (GH-ZZW30) | Ryouzanpaku With Apr | 1:50.5190 |
| 22nd | 46 | Kota Sasaki / Taku Bamba | Nissan Fairlady Z (Z33) | Mola | 1:51.1320 |
| 23rd | 11 | Tetsuya Tanaka / Takayuki Aoki | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:51.5220 |
| 24th | 62 | Shinsuke Shibahara / Haruki Kurosawa | Vemac RD408R | Willcom R&D Sport | 1:51.1730 |
| 25th | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 1:51.5520 |
| 26th | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 1:51.2160 |
| 27th | 55 | Hidetoshi Mitsusada / Daisuke Ikeda | Ford GT (DHG-replica) | Dhg Racing | 1:51.6590 |
| 28th | 61 | Shogo Mitsuyama / Nobuteru Taniguchi | Vemac RD320R | R&D Sport | 1:51.8360 |
| 29th | 47 | Masaoki Nagashima / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 1:52.1900 |
| 30th | 110 | Hideshi Matsuda / Ichijou Suga | Porsche 986 Boxster | Arktech Motorsports | 1:52.2090 |
| 31st | 77 | Katsuo Kobayashi / Yasushi Kikuchi | Subaru Impreza (GD) | Cusco Racing | 1:52.4350 |
| 32nd | 88 | Marco Apicella / Yasutaka Hinoi | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:52.6680 |
| 33rd | 52 | Hironori Takeuchi / Kouki Saga | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:53.1160 |
| 34th | 9 | Osamu Nakajima / Masaki Tanaka | Mosler MT900R | A&S Racing | 1:53.2380 |
| 35th | 14 | Mitsuhiro Kinoshita / Kyousuke Mineo | Porsche 996 GT3-RS | Endless Sports | 1:53.4780 |
| 36th | 87 | Kouji Yamanishi / Hisashi Wada | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:53.5160 |
| 37th | 19 | Kouji Matsuda / Shigekazu Wakisaka | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:53.7130 |