| 1st | 38 | Yuuji Tachikawa / Richard Lyons | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:45.7490 |
| 2nd | 1 | Ralph Firman / Takuya Izawa | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:45.8070 |
| 3rd | 32 | Loïc Duval / Katsuyuki Hiranaka | Honda NSX (LA-NA2) | Nakajima Racing | 1:46.0230 |
| 4th | 6 | Akira Iida / Roberto Streit / Björn Wirdheim | Lexus SC430 (UZZ40) | Eneos Toyota Team Le Mans | 1:46.1340 |
| 5th | 100 | Yuuji Ide / Shin'ya Hosokawa / Kousuke Matsuura | Honda NSX (LA-NA2) | Team Kunimitsu | 1:46.6760 |
| 6th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Dome Racing Team | 1:46.7030 |
| 7th | 36 | Carlo van Dam / Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Petronas Toyota Team Tom's | 1:46.7660 |
| 8th | 17 | Katsutomo Kaneishi / Toshihiro Kaneishi / Koudai Tsukakoshi | Honda NSX (LA-NA2) | Real Racing With Leon | 1:46.8330 |
| 9th | 35 | Peter Dumbreck / Tatsuya Kataoka | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:46.9310 |
| 10th | 12 | Tsugio Matsuda / Sébastien Philippe | Nissan GT-R | Team Impul | 1:47.3550 |
| 11th | 25 | Pierre Kaffer / Takeshi Tsuchiya / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:47.4970 |
| 12th | 3 | Ronnie Quintarelli / Naoki Yokomizo | Nissan GT-R | Hasemi Motorsport | 1:47.5860 |
| 13th | 39 | Toranosuke Takagi / André Couto / Kouki Saga | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:47.8160 |
| 14th | 22 | Michael Krumm / Dominik Schwager / Masataka Yanagida | Nissan GT-R | Nismo | 1:48.1670 |
| 15th | 24 | Seiji Ara / Joao Paolo de Oliveira | Nissan GT-R | Kondo Racing | 1:48.5380 |
| 16th | 23 | Satoshi Motoyama / Benoit Tréluyer / Fabio Carbone | Nissan GT-R | Nismo | 1:48.6770 |
| 17th | 66 | Kouji Yamanishi / Atsushi Yogou | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:56.2640 |
| 18th | 33 | Mitsuhiro Kinoshita / Masami Kageyama | Porsche 997 GT3 RSR | Hankook KTR | 1:56.5800 |
| 19th | 26 | Nobuteru Taniguchi / Shin'ichi Yamaji / Keita Sawa | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 1:56.8670 |
| 20th | 19 | Manabu Orido / Tsubasa Abe / Yuuhi Sekiguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:56.8700 |
| 21st | 2 | Kazuho Takahashi / Hiroki Katou | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:56.9000 |
| 22nd | 52 | Takuya Kurosawa / Takuto Iguchi / Hideki Yamauchi | Lexus IS350 (GSE21) | Team Takeuchi With Shift | 1:57.0730 |
| 23rd | 46 | Kazuki Hoshino / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 1:57.1920 |
| 24th | 81 | Takayuki Aoki / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Team Daishin | 1:57.4320 |
| 25th | 7 | Hiroyuki Iiri / Ryou Orime / Hiroyuki Matsumura | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:57.4960 |
| 26th | 77 | Tetsuya Yamano / Kota Sasaki | Subaru Impreza (GD) | Cusco Racing | 1:57.6030 |
| 27th | 11 | Tetsuya Tanaka / Masayuki Ueda | Ferrari F430 (GF-F360) | Jim Gainer | 1:57.7600 |
| 28th | 111 | Hiroshi Koizumi / Tsubasa Kurosawa / Paul Yip / Hidetoshi Mitsusada | Porsche 986 Boxster | Arktech Motorsports | 1:57.8670 |
| 29th | 4 | Ryohei Sakaguchi / Masaki Matsushita / Tadao Uematsu | Vemac RD320R | Team Uematsu Nova | 1:57.9320 |
| 30th | 43 | Morio Nitta / Shinichi Takagi / Kyousuke Mineo | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:58.6280 |
| 31st | 87 | Hisashi Wada / Muneyuki Kurihara / Yoshihisa Namekata | Lamborghini Gallardo RG-3 | JLOC | 1:58.9680 |
| 32nd | 666 | Syougo Suhou / Jun'ichirou Yamashita / Megumi Inoue / "Takamori.com" | Vemac RD320R | Avanzza Rosso | 1:59.9930 |
| 33rd | 118 | Takshi Miyamoto / Masayuki Kurihara / Masaki Jounai | Porsche 996 GT3-RS | Tomei Sports | 2:00.4520 |