| 1st | 39 | Takuto Iguchi / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:34.1220 |
| 2nd | 38 | Kouhei Hirate / Yuuji Tachikawa | Lexus SC430 (UZZ40) | Lexus Team Zent Cerumo | 1:34.5250 |
| 3rd | 6 | Kazuya Oshima / Daisuke Itou | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:34.6880 |
| 4th | 35 | André Couto / Juichi Wakisaka | Lexus SC430 (UZZ40) | Lexus Team Kraft | 1:34.7080 |
| 5th | 36 | Andre Lotterer / Kazuki Nakajima | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:34.7450 |
| 6th | 8 | Hideki Mutou / Takashi Kobayashi | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:35.3150 |
| 7th | 46 | Ronnie Quintarelli / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:34.3500 |
| 8th | 1 | Loic Duval / Takashi Kogure | Honda HSV-010 GT (H010) | weider Honda Racing | 1:35.3410 |
| 9th | 32 | Ryou Michigami / Yuuki Nakayama | Honda HSV-010 GT (H010) | Nakajima Racing | 1:35.5140 |
| 10th | 17 | Toshihiro Kaneishi / Koudai Tsukakoshi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:35.2740 |
| 11th | 23 | Benoit Tréluyer / Satoshi Motoyama | Nissan GT-R (R35) | Nismo | 1:35.5610 |
| 12th | 24 | Hironobu Yasuda / Björn Wirdheim | Nissan GT-R (R35) | Kondo Racing | 1:35.6370 |
| 13th | 12 | Joao Paolo de Oliveira / Tsugio Matsuda | Nissan GT-R (R35) | Team Impul | 1:35.6470 |
| 14th | 19 | Seiji Ara / Tatsuya Kataoka | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:35.8470 |
| 15th | 100 | Takuya Izawa / Naoki Yamamoto | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:35.8680 |
| 17th | 4 | Nobuteru Taniguchi / Taku Bamba | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:43.4160 |
| 18th | 26 | Hideshi Matsuda / Kyousuke Mineo | Porsche 996 GT3-R | Team Taisan Cinecitta | 1:43.7960 |
| 19th | 2 | Hiroki Katou / Kazuho Takahashi | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:44.1350 |
| 20th | 25 | Akihiro Tsuduki / Takeshi Tsuchiya | Porsche 997 GT3 RSR | Samurai Team Tsuchiya | 1:44.4440 |
| 21st | 88 | Hiroyuki Iiri / Yuuhi Sekiguchi | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:43.8200 |
| 22nd | 43 | Shinichi Takagi / Kousuke Matsuura | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:44.5120 |
| 23rd | 5 | Haruki Kurosawa / Tetsuji Tamanaka | Vemac RD320R | Team Mach | 1:44.3300 |
| 24th | 14 | Ryou Orime / Alexandre Imperatori | Lexus IS350 (GSE21) | Team SG Changi | 1:44.5670 |
| 25th | 41 | Shin'ichi Yamaji / Hiroshi Koizumi | Ferrari F430 GT | Team Taisan Cinecitta | 1:44.6100 |
| 26th | 15 | Yasuhiro Shimizu / Tim Bergmeister | Porsche 997 GT3 R | Team Art Taste | 1:44.6460 |
| 27th | 86 | Takayuki Aoki / Yuuya Sakamoto | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:44.6780 |
| 28th | 27 | Hideki Yamauchi / Yutaka Yamagishi | Ferrari F430 GTC | LMP Motorsport | 1:44.7240 |
| 29th | 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 1:44.7580 |
| 30th | 87 | Manabu Orido / Atsushi Yogou | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:45.0640 |
| 31st | 62 | Tetsuya Yamano / Kota Sasaki | Subaru Legacy B4 (BM9) | R&D Sport | 1:45.0850 |
| 32nd | 11 | Tetsuya Tanaka / Katsuyuki Hiranaka | Ferrari 458 GTC | Jim Gainer | 1:45.1680 |
| 33rd | 66 | Kazuki Hoshino / Hiroki Yoshimoto | Aston Martin V8 Vantage GT2 | A Speed | 1:45.3920 |
| 34th | 69 | Hiroki Yoshida / Melvin Choo | Mosler MT900M | Thunder Asia Racing | 1:45.4150 |
| 35th | 31 | Yuuki Iwasaki / Kouki Saga | Toyota Corolla Axio (NZE141) | Apr | 1:45.6470 |
| 36th | 10 | Masayuki Ueda / Masataka Kawaguchi | Ferrari F430 | Jim Gainer | 1:45.6550 |
| 37th | 7 | Carlo van Dam / Akira Mizutani | Porsche 997 GT3 R | Direction Racing | 1:45.7160 |
| 38th | 74 | Morio Nitta / Yuuji Kunimoto | Toyota Corolla Axio (NZE141) | Apr | 1:45.8160 |
| 39th | 34 | Hiroshi Takamori / Michael Kim | Porsche 997 GT3 RSR | Hankook KTR | 1:48.3340 |