| 1st | 18 | Ryō Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Dome Racing Team | 1:33.6970 |
| 2nd | 1 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:34.3430 |
| 3rd | 8 | Daisuke Ito / Ralph Firman | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:34.2610 |
| 4th | 17 | Katsutomo Kaneishi / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Rolling Stone Real Racing | 1:34.3510 |
| 5th | 12 | Benoit Tréluyer / Kazuki Hoshino | Nissan Fairlady Z (Z33) | Team Impul | 1:34.4720 |
| 6th | 38 | Yuji Tachikawa / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:34.4550 |
| 7th | 32 | Loïc Duval / Fabio Carbone | Honda NSX (LA-NA2) | Nakajima Racing | 1:34.4210 |
| 8th | 39 | André Couto / Katsuyuki Hiranaka | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:34.3890 |
| 9th | 100 | Shin'ya Hosokawa / Dominik Schwager | Honda NSX (LA-NA2) | Team Kunimitsu | 1:34.4280 |
| 10th | 25 | Takeshi Tsuchiya / Manabu Orido | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:34.3890 |
| 11th | 23 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:34.5820 |
| 12th | 35 | Naoki Hattori / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:34.7370 |
| 13th | 22 | Michael Krumm / Tsugio Matsuda | Nissan Fairlady Z (Z33) | Nismo | 1:34.7850 |
| 14th | 6 | Tatsuya Kataoka / Björn Wirdheim | Lexus SC430 (UZZ40) | Forum Eng. Toyota Team Le Mans | 1:34.8190 |
| 15th | 3 | Sébastien Philippe / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:34.9300 |
| 16th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan Fairlady Z (Z33) | Kondo Racing | 1:35.1180 |
| 17th | 88 | Marco Apicella / Koji Yamanishi | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:42.5150 |
| 18th | 33 | Mitsuhiro Kinoshita / Yuuya Sakamoto | Porsche 996 GT3-R | Hankook Ktr | 1:42.9630 |
| 19th | 2 | Kazuho Takahashi / Hiroki Kato | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:42.9540 |
| 20th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 1:42.5970 |
| 21st | 26 | Shinichi Yamaji / Nobuteru Taniguchi | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 1:42.9300 |
| 22nd | 46 | Kota Sasaki / Naoki Yokomizo | Nissan Fairlady Z (Z33) | Mola | 1:42.9680 |
| 23rd | 7 | Hiroyuki Iiri / Ryou Orime | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:43.2200 |
| 24th | 101 | Kazuya Oshima / Hiroaki Ishiura | Toyota MR-S (GH-ZZW30) | Apr | 1:43.0890 |
| 25th | 62 | Shinsuke Shibahara / Haruki Kurosawa | Vemac RD408R | Willcom R&D Sport | 1:43.2110 |
| 26th | 31 | Kyousuke Mineo / Yuuya Sakamoto | Toyota MR-S (GH-ZZW30) | Apr | 1:43.2810 |
| 27th | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 1:43.3170 |
| 28th | 9 | Osamu Nakajima / Masaki Jounai | Mosler MT900R (OOX) | A&S Racing | 1:43.3290 |
| 29th | 47 | Shigekazu Wakisaka / Shogo Mitsuyama | Nissan Fairlady Z (Z33) | Mola | 1:43.3790 |
| 30th | 4 | Tetsuya Tanaka / Shinsuke Yamazaki | Vemac RD350R | Ebbro Team Nova | 1:43.4390 |
| 31st | 77 | Tetsuya Yamano / Takayuki Aoki | Subaru Impreza (GD) | Cusco Racing | 1:43.4410 |
| 32nd | 87 | Yasutaka Hinoi / Atsushi Yogo | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:43.5460 |
| 33rd | 55 | Daisuke Ikeda / Taku Bamba | Ford GT (DHG-replica) | Dhg Racing | 1:43.7910 |
| 34th | 5 | Tetsuji Tamanaka / Hironori Takeuchi | Vemac RD320R | Team Mach | 1:43.7960 |
| 35th | 83 | Tadao Uematsu / Ryohei Sakaguchi | Vemac RD320R | Yokoyama Racing | 1:43.9130 |
| 36th | 19 | Akira Iida / Yuhi Sekiguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:44.0420 |
| 37th | 11 | Masayuki Ueda / Hideshi Matsuda | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:44.1450 |
| 38th | 666 | Syougo Suhou / Jun'ichirou Yamashita | Vemac RD320R | Avanzza x Bomex | 1:44.6740 |
| 39th | 333 | Katsuo Kobayashi / Takashi Inoue | Porsche 996 GT3-RSR | Mario Racing With Ishimatsu | 1:45.3870 |
| 40th | 70 | Yoshimi Ishibashi / Hiroshi Koizumi | Porsche 996 GT3-RS | Team Gaikokuya | 1:46.0230 |
| 41st | 118 | Takshi Miyamoto / Syouzou Tagahara | Porsche 996 GT3-RS | Tomei Sports | 1:46.4400 |
| 42nd | 66 | Naohiro Furuya / Muneyuki Kurihara | Lamborghini Gallardo RG-3 | JLOC | 1:49.5620 |
| 43rd | 110 | Takuya Kurosawa / Hidetoshi Mitsusada | Porsche 986 Boxster | Arktech Motorsports | 1:46.0260 |
| 44th | 111 | Yasushi Kikuchi / Takaya Tsubobayashi | Porsche 986 Boxster | Arktech Motorsports | 1:46.1420 |
| 45th | 67 | Tsubasa Kurosawa / Hisashi Wada | Lamborghini Gallardo RG-3 | JLOC | 1:51.8330 |