| 1st | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Dome Racing Team | 1:34.0320 |
| 2nd | 8 | Daisuke Itou / Ralph Firman | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:34.1830 |
| 3rd | 23 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:34.4530 |
| 4th | 22 | Michael Krumm / Tsugio Matsuda | Nissan Fairlady Z (Z33) | Nismo | 1:34.4670 |
| 5th | 1 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:34.5140 |
| 6th | 100 | Shin'ya Hosokawa / Dominik Schwager | Honda NSX (LA-NA2) | Team Kunimitsu | 1:34.5960 |
| 7th | 39 | André Couto / Katsuyuki Hiranaka | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:34.6420 |
| 8th | 38 | Yuuji Tachikawa / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:34.7680 |
| 9th | 35 | Naoki Hattori / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:34.8000 |
| 10th | 99 | | Honda NSX (LA-NA2) | | 1:34.9330 |
| 11th | 25 | Takeshi Tsuchiya / Manabu Orido | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:35.0530 |
| 12th | 32 | Loic Duval / Fabio Carbone | Honda NSX (LA-NA2) | Nakajima Racing | 1:35.0730 |
| 13th | 17 | Katsutomo Kaneishi / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Rolling Stone Real Racing | 1:35.1800 |
| 14th | 6 | Tatsuya Kataoka / Björn Wirdheim | Lexus SC430 (UZZ40) | Forum Eng. Toyota Team Le Mans | 1:35.2780 |
| 15th | 88 | Yasutaka Hinoi / Atsushi Yogou / Kouji Yamanishi | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:39.6570 |
| 16th | 26 | Shin'ichi Yamaji / Nobuteru Taniguchi | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 1:42.7110 |
| 17th | 62 | Shinsuke Shibahara / Haruki Kurosawa | Vemac RD408R | Willcom R&D Sport | 1:42.9590 |
| 18th | 4 | Tetsuya Tanaka / Shinsuke Yamazaki | Vemac RD350R | Ebbro Team Nova | 1:42.9850 |
| 19th | 19 | Akira Iida / Yuuhi Sekiguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:43.0180 |
| 20th | 2 | Kazuho Takahashi / Hiroki Katou | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:43.0410 |
| 21st | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 1:43.1000 |
| 22nd | 31 | Kyousuke Mineo / Yuuya Sakamoto / Kazuya Oshima / Hiroaki Ishiura | Toyota MR-S (GH-ZZW30) | Apr | 1:43.2320 |
| 23rd | 11 | Masayuki Ueda / Hideshi Matsuda | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:43.4030 |
| 24th | 33 | Mitsuhiro Kinoshita / Yuuya Sakamoto | Porsche 996 GT3-R | Hankook Ktr | 1:43.4190 |
| 25th | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 1:43.5070 |
| 26th | 46 | Kota Sasaki / Naoki Yokomizo | Nissan Fairlady Z (Z33) | Mola | 1:43.7180 |
| 27th | 110 | Takuya Kurosawa / Hidetoshi Mitsusada | Porsche 986 Boxster | Arktech Motorsports | 1:43.7550 |
| 28th | 47 | Shigekazu Wakisaka / Shogo Mitsuyama | Nissan Fairlady Z (Z33) | Mola | 1:44.3470 |
| 29th | 9 | "Osamu" / Masaki Jounai | Mosler MT900R (OOX) | A&S Racing | 1:44.5580 |
| 30th | 55 | Daisuke Ikeda / Taku Bamba | Ford GT (DHG-replica) | Dhg Racing | 1:44.6700 |
| 31st | 77 | Tetsuya Yamano / Takayuki Aoki | Subaru Impreza (GD) | Cusco Racing | 1:44.7230 |
| 32nd | 666 | Syougo Suhou / Jun'ichirou Yamashita | Vemac RD320R | Avanzza x Bomex | 1:45.2680 |
| 33rd | 118 | Takshi Miyamoto / Syouzou Tagahara | Porsche 996 GT3-RS | Tomei Sports | 1:45.7440 |
| 34th | 66 | Naohiro Furuya / Muneyuki Kurihara | Lamborghini Gallardo RG-3 | JLOC | 1:46.0390 |
| 35th | 67 | Tsubasa Kurosawa / Hisashi Wada | Lamborghini Gallardo RG-3 | JLOC | 3:24.1740 |