| 1st | 38 | Toranosuke Takagi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:54.2560 |
| 2nd | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:53.8820 |
| 3rd | 37 | Tatsuya Kataoka / Sakon Yamamoto | Toyota Supra (JZA80) | Toyota Team Tom's | 1:54.3900 |
| 4th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Honda Racing | 1:54.5060 |
| 5th | 32 | Andre Lotterer / Tsugio Matsuda | Honda NSX (LA-NA2) | Nakajima Racing | 1:54.5040 |
| 6th | 8 | Ralph Firman / Daisuke Itou | Honda NSX (LA-NA2) | Team Honda Racing | 1:54.5490 |
| 7th | 3 | Erik Comas / Toshihiro Kaneishi | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:54.6770 |
| 8th | 100 | Sébastien Philippe / Jeremie Dufour | Honda NSX (LA-NA2) | Team Kunimitsu | 1:55.1170 |
| 9th | 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:55.4700 |
| 10th | 22 | Masataka Yanagida / Michael Krumm | Nissan Fairlady Z (Z33) | NISMO | 1:55.1630 |
| 11th | 34 | Seiji Ara / Naoki Yokomizo | Toyota Supra (JZA80) | KRAFT | 1:55.5170 |
| 12th | 25 | Manabu Orido / Dominik Schwager | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:55.5780 |
| 13th | 36 | James Courtney / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Team Tom's | 1:55.6500 |
| 14th | 35 | Peter Dumbreck / Naoki Hattori | Toyota Supra (JZA80) | KRAFT | 1:55.7550 |
| 15th | 21 | Takuya Kurosawa / Hidetoshi Mitsusada | Ferrari 550 Maranello | Hitotsuyama Racing | 1:58.3210 |
| 16th | 39 | André Couto / Ronnie Quintarelli | Toyota Supra (JZA80) | Toyota Team SARD | no time |
| 17th | 12 | Benoit Tréluyer / Yuuji Ide | Nissan Fairlady Z (Z33) | Team Impul | no time |
| 19th | 31 | Minoru Tanaka / Kazuki Nakajima | Toyota MR-S (GH-ZZW30) | Kicchouhouzan With Apr | 2:04.2960 |
| 20th | 2 | Kazuho Takahashi / Akira Watanabe | Vemac RD320R | Verno Tokai Dream 28 | 2:04.3690 |
| 21st | 0 | Haruki Kurosawa / Shin'ya Hosokawa | Honda NSX (LA-NA2) | M-Tec Co. Ltd. | 2:04.9780 |
| 22nd | 27 | Hiroki Yoshimoto / Shogo Mitsuyama | Vemac RD320R | Direxiv Motorsports | 2:04.8930 |
| 23rd | 47 | Tomonobu Fujii / Gou Shimizu | Nissan Fairlady Z (Z33) | Mola | 2:05.0120 |
| 24th | 13 | Masami Kageyama / Mitsuhiro Kinoshita | Nissan Fairlady Z (Z33) | Endless Sports | 2:05.3010 |
| 25th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 2:05.0670 |
| 26th | 11 | Tetsuya Tanaka / Paolo Montin | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:05.1070 |
| 27th | 62 | Tadao Uematsu / Shinsuke Shibahara | Vemac RD350R | Willcom R&D Sport | 2:05.0170 |
| 28th | 19 | Nobuteru Taniguchi / Hiroki Katou | Toyota Celica (ZZT231) | Racing Project Bandoh | 2:05.5130 |
| 29th | 77 | Tatsuya Tanigawa / Katsuo Kobayashi | Subaru Impreza (GDB) | Cusco Racing | 2:05.3130 |
| 30th | 46 | Kazuki Hoshino / Takayuki Aoki | Nissan Fairlady Z (Z33) | Mola | 2:05.5770 |
| 31st | 7 | Hiroyuki Iiri / Shin'ichi Yamaji | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:05.7610 |
| 32nd | 30 | Kota Sasaki / Tetsuya Yamano | Toyota MR-S (GH-ZZW30) | Team Reckless | 2:05.7960 |
| 33rd | 86 | Kouji Yamanishi / Naohiro Furuya | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 2:05.9600 |
| 34th | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 2:06.6870 |
| 35th | 87 | Marco Apicella / Hisashi Wada | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 2:06.8980 |
| 36th | 52 | Hironori Takeuchi / Katsuyuki Hiranaka | Toyota Celica (ZZT231) | Toyota Team Cerumo | 2:06.9450 |
| 37th | 110 | Takashi Ooi / Ichijou Suga | Porsche 986 Boxster | Arktech Motorsports | 2:07.1630 |
| 38th | 10 | Hideshi Matsuda / Yasutaka Hinoi | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:07.7620 |
| 39th | 112 | Atsushi Yogou / Takaya Tsubobayashi | Porsche 996 GT3 | Arktech Motorsports | 2:08.1590 |
| 40th | 26 | Yutaka Yamagishi / Isao Ihashi | Porsche 996 GT3-RS | Team Taisan Advan | 2:08.2610 |
| 41st | 777 | Kazuyoshi Takamizawa / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 2:08.6880 |
| 42nd | 111 | Hiroya Iijima / Masaki Jounai | Porsche 968 (E-968) | Team LeyJun | 2:10.1480 |
| 43rd | 9 | Jun'ichirou Yamashita / Syougo Suhou | Mosler MT900R | A&S Racing | 2:10.7410 |
| 44th | 170 | Yoshimi Ishibashi / Takashi Inoue | Porsche 996 GT3-RS | Team Gaikokuya | 2:11.1160 |
| 45th | 72 | Hiroshi Wada / Akira Hirakawa | Porsche 996 GT3-RSR | Teramoto Technical Office | 2:13.6220 |