| 1st | 6 | Daisuke Itou / Björn Wirdheim | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:44.8410 |
| 2nd | 35 | Kazuya Oshima / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Kraft | 1:45.4080 |
| 3rd | 18 | Loïc Duval / Takashi Kogure | Honda HSV-010 GT (H010) | weider Honda Racing | 1:45.7710 |
| 4th | 1 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:45.8710 |
| 5th | 12 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | Team Impul | 1:45.9700 |
| 6th | 17 | Toshihiro Kaneishi / Koudai Tsukakoshi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:46.5450 |
| 7th | 24 | Joao Paolo de Oliveira / Hironobu Yasuda | Nissan GT-R (R35) | Kondo Racing | 1:46.5830 |
| 8th | 38 | Yuuji Tachikawa / Richard Lyons | Lexus SC430 (UZZ40) | Lexus Team Zent Cerumo | 1:46.6200 |
| 9th | 8 | Ralph Firman / Yuuji Ide | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:46.9200 |
| 10th | 100 | Takuya Izawa / Naoki Yamamoto | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:47.1640 |
| 11th | 23 | Satoshi Motoyama / Benoit Tréluyer | Nissan GT-R (R35) | Nismo | 1:47.3830 |
| 12th | 32 | Ryou Michigami / Yuuki Nakayama | Honda HSV-010 GT (H010) | Nakajima Racing | 1:47.5060 |
| 13th | 39 | Carlo van Dam / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:48.0390 |
| 14th | 66 | Hideshi Matsuda / Hiroki Yoshimoto | Aston Martin V8 Vantage GT2 | A Speed | 1:56.3460 |
| 15th | 2 | Hiroki Katou / Hiroshi Hamaguchi | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:56.4710 |
| 16th | 46 | Naoki Yokomizo / Tsubasa Abe | Nissan Fairlady Z (Z33) | Mola | 1:56.5720 |
| 17th | 25 | Akihiro Tsuduki / Takeshi Tsuchiya | Porsche 997 GT3 RSR | Samurai Team Tsuchiya | 1:56.6010 |
| 18th | 86 | Kouji Yamanishi / Yuuhi Sekiguchi | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:56.8280 |
| 19th | 11 | Tetsuya Tanaka / Katsuyuki Hiranaka | Ferrari F430 | Jim Gainer | 1:56.8510 |
| 20th | 5 | Tetsuji Tamanaka / Haruki Kurosawa | Vemac RD408R | Team Mach | 1:56.9170 |
| 21st | 88 | Atsushi Yogou / Tsubasa Kurosawa | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:56.9460 |
| 22nd | 19 | Manabu Orido / Tatsuya Kataoka | Lexus IS350 (GSE21) | Racing Project Bandoh | 1:56.9860 |
| 23rd | 74 | Takuto Iguchi / Yuuji Kunimoto | Toyota Corolla Axio (NZE141) | Apr | 1:57.0230 |
| 24th | 3 | Kazuki Hoshino / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motor Sport | 1:57.0850 |
| 25th | 27 | Yutaka Yamagishi / Hiroshi Koizumi | Ferrari F430 GTC | LMP Motorsport | 1:57.2180 |
| 26th | 28 | Yuuki Iwasaki / Akihiko Asai | Porsche 996 GT3-RSR | LMP Motorsport | 1:57.3780 |
| 27th | 62 | Tetsuya Yamano / Kota Sasaki | Subaru Legacy B4 (BM9) | R&D Sport | 1:57.3880 |
| 28th | 7 | Nobuteru Taniguchi / Ryou Orime | Mazda RX-7 (FD3S) | M7 RE Amemiya Racing | 1:57.4410 |
| 29th | 26 | Masayuki Ueda / Shogo Mitsuyama | Porsche 996 GT3-R | Team Taisan | 1:57.4640 |
| 30th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:57.7210 |
| 31st | 31 | Kouki Saga / Kousuke Matsuura | Toyota Corolla Axio (NZE141) | Apr | 1:57.9050 |
| 32nd | 9 | Taku Bamba / Masahiro Sasaki | Porsche 997 GT3 RSR | Good Smile Racing With Cox | 1:58.6660 |
| 33rd | 87 | Hiroyuki Iiri / Yuuya Sakamoto | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:58.9520 |
| 34th | 51 | Yuuya Sakamoto / Hideki Yamauchi | Porsche 996 GT3-RS | Team Taisan | 1:59.0880 |
| 35th | 360 | Atsushi Tanaka / Masahiro Matsunaga | Porsche 996 GT3-RSR | Tomei Sports | 1:59.8960 |
| 36th | 22 | Hisashi Wada / Masaki Jounai | Vemac RD350R | R'Qs Motorsports | 2:00.2100 |
| 37th | 666 | Jun'ichirou Yamashita / "Takamori.com" | Porsche 986 Boxster | Bomex Rosso | 2:01.4230 |