| 1st | 8 | Daisuke Itou / Ralph Firman | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:50.4260 |
| 2nd | 32 | Loïc Duval / Fabio Carbone | Honda NSX (LA-NA2) | Nakajima Racing | 1:51.5230 |
| 3rd | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Dome Racing Team | 1:51.0480 |
| 4th | 17 | Katsutomo Kaneishi / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Rolling Stone Real Racing | 1:51.2010 |
| 5th | 38 | Yuuji Tachikawa / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:51.9690 |
| 6th | 100 | Shin'ya Hosokawa / Dominik Schwager | Honda NSX (LA-NA2) | Team Kunimitsu | 1:52.3710 |
| 7th | 23 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:51.8980 |
| 8th | 6 | Tatsuya Kataoka / Björn Wirdheim | Lexus SC430 (UZZ40) | Forum Eng. Toyota Team Le Mans | 1:52.4600 |
| 9th | 22 | Michael Krumm / Tsugio Matsuda | Nissan Fairlady Z (Z33) | Nismo | 1:52.2930 |
| 10th | 39 | André Couto / Katsuyuki Hiranaka | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:52.8770 |
| 11th | 1 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:52.9400 |
| 12th | 35 | Naoki Hattori / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:53.0850 |
| 13th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan Fairlady Z (Z33) | Kondo Racing | 1:53.6430 |
| 14th | 12 | Benoit Tréluyer / Kazuki Hoshino | Nissan Fairlady Z (Z33) | Team Impul | 1:54.0480 |
| 15th | 3 | Sébastien Philippe / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:54.1740 |
| 16th | 25 | Takeshi Tsuchiya / Manabu Orido | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:55.5420 |
| 17th | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 2:02.5360 |
| 18th | 101 | Kazuya Oshima / Hiroaki Ishiura | Toyota MR-S (GH-ZZW30) | Apr | 2:02.9230 |
| 19th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 2:03.4070 |
| 20th | 46 | Kota Sasaki / Naoki Yokomizo | Nissan Fairlady Z (Z33) | Mola | 2:03.7260 |
| 21st | 2 | Kazuho Takahashi / Hiroki Katou | Shiden MC/RT-16 | Cars Tokai Dream28 | 2:03.0380 |
| 22nd | 62 | Shinsuke Shibahara / Haruki Kurosawa | Vemac RD408R | Willcom R&D Sport | 2:03.1800 |
| 23rd | 88 | Marco Apicella / Kouji Yamanishi | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 2:04.1730 |
| 24th | 31 | Kyousuke Mineo / Yuuya Sakamoto | Toyota MR-S (GH-ZZW30) | Apr | 2:04.3810 |
| 25th | 7 | Hiroyuki Iiri / Ryou Orime | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:04.0340 |
| 26th | 87 | Yasutaka Hinoi / Atsushi Yogou | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 2:04.5090 |
| 27th | 4 | Tetsuya Tanaka / Shinsuke Yamazaki | Vemac RD350R | Ebbro Team Nova | 2:04.7140 |
| 28th | 26 | Shin'ichi Yamaji / Nobuteru Taniguchi | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 2:04.7210 |
| 29th | 47 | Shigekazu Wakisaka / Shogo Mitsuyama | Nissan Fairlady Z (Z33) | Mola | 2:04.9800 |
| 30th | 110 | Takuya Kurosawa / Hidetoshi Mitsusada | Porsche 986 Boxster | Arktech Motorsports | 2:05.1800 |
| 31st | 5 | Tetsuji Tamanaka / Hironori Takeuchi | Vemac RD320R | Team Mach | 2:05.3460 |
| 32nd | 19 | Akira Iida / Yuuhi Sekiguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 2:05.3580 |
| 33rd | 77 | Tetsuya Yamano / Takayuki Aoki | Subaru Impreza (GD) | Cusco Racing | 2:05.4690 |
| 34th | 11 | Masayuki Ueda / Hideshi Matsuda | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:05.6350 |
| 35th | 83 | Tadao Uematsu / Ryohei Sakaguchi | Vemac RD320R | Yokoyama Racing | 2:05.7670 |
| 36th | 55 | Daisuke Ikeda / Taku Bamba | Ford GT (DHG-replica) | Dhg Racing | 2:05.9560 |
| 37th | 666 | Syougo Suhou / Jun'ichirou Yamashita | Vemac RD320R | Avanzza x Bomex | 2:07.2390 |
| 38th | 333 | Katsuo Kobayashi / Takashi Inoue | Porsche 996 GT3-RSR | Mario Racing With Ishimatsu | 2:07.8330 |
| 39th | 9 | Osamu Nakajima / Masaki Jounai | Mosler MT900R (OOX) | A&S Racing | 2:09.4690 |
| 40th | 118 | Takshi Miyamoto / Syouzou Tagahara | Porsche 996 GT3-RS | Tomei Sports | 2:09.8790 |
| 41st | 70 | Hiroshi Koizumi / Kazuyoshi Takamizawa | Porsche 996 GT3-RS | Team Gaikokuya | 2:17.2060 |