| 1st | 46 | Ronnie Quintarelli / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:39.6070 |
| 2nd | 39 | Takuto Iguchi / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:40.4860 |
| 3rd | 17 | Toshihiro Kaneishi / Koudai Tsukakoshi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:40.5180 |
| 4th | 1 | Loic Duval / Takashi Kogure | Honda HSV-010 GT (H010) | weider Honda Racing | 1:40.5270 |
| 5th | 35 | André Couto / Juichi Wakisaka | Lexus SC430 (UZZ40) | Lexus Team Kraft | 1:40.7150 |
| 6th | 6 | Kazuya Oshima / Daisuke Itou | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:40.7320 |
| 7th | 12 | Joao Paolo de Oliveira / Tsugio Matsuda | Nissan GT-R (R35) | Team Impul | 1:40.8070 |
| 8th | 100 | Takuya Izawa / Naoki Yamamoto | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:40.8650 |
| 9th | 8 | Hideki Mutou / Takashi Kobayashi | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:41.4570 |
| 10th | 24 | Hironobu Yasuda / Björn Wirdheim | Nissan GT-R (R35) | Kondo Racing | 1:41.4600 |
| 11th | 38 | Kouhei Hirate / Yuuji Tachikawa | Lexus SC430 (UZZ40) | Lexus Team Zent Cerumo | 1:41.8670 |
| 12th | 36 | Andre Lotterer / Kazuki Nakajima | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:41.9200 |
| 13th | 23 | Satoshi Motoyama / Benoit Tréluyer | Nissan GT-R (R35) | Nismo | 1:42.4200 |
| 14th | 32 | Yuuki Nakayama / Ryou Michigami | Honda HSV-010 GT (H010) | Nakajima Racing | 1:42.5430 |
| 15th | 19 | Tatsuya Kataoka / Seiji Ara | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:42.9750 |
| 17th | 25 | Takeshi Tsuchiya / Akihiro Tsuduki | Porsche 997 GT3 RSR | Samurai Team Tsuchiya | 1:51.0010 |
| 18th | 2 | Hiroki Katou / Kazuho Takahashi | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:51.2650 |
| 19th | 11 | Tetsuya Tanaka / Katsuyuki Hiranaka | Ferrari 458 GTC | Jim Gainer | 1:51.3850 |
| 20th | 43 | Kousuke Matsuura / Shinichi Takagi | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:51.4380 |
| 21st | 86 | Yuuya Sakamoto / Takayuki Aoki | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:51.7290 |
| 22nd | 74 | Morio Nitta / Yuuji Kunimoto | Toyota Corolla Axio (NZE141) | Apr | 1:51.7430 |
| 23rd | 62 | Tetsuya Yamano / Kota Sasaki | Subaru Legacy B4 (BM9) | R&D Sport | 1:51.9970 |
| 24th | 87 | Manabu Orido / Atsushi Yogou | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:52.0260 |
| 25th | 31 | Yuuki Iwasaki / Kouki Saga | Toyota Corolla Axio (NZE141) | Apr | 1:52.2680 |
| 26th | 4 | Nobuteru Taniguchi / Taku Bamba | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:52.4640 |
| 27th | 27 | Yutaka Yamagishi / Carlo van Dam | Ferrari F430 GTC | LMP Motorsport | 1:52.5460 |
| 28th | 22 | Hisashi Wada / Masaki Jounai | Vemac RD350R | R'Qs Motorsports | 1:52.5590 |
| 29th | 15 | Yasuhiro Shimizu / Tim Bergmeister | Porsche 997 GT3 R | Team Art Taste | 1:52.7620 |
| 30th | 14 | Ryou Orime / Alexandre Imperatori | Lexus IS350 (GSE21) | Team SG Changi | 1:52.8600 |
| 31st | 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 1:52.8820 |
| 32nd | 66 | Kazuki Hoshino / Hiroki Yoshimoto | Aston Martin V8 Vantage GT2 | A Speed | 1:53.0210 |
| 33rd | 26 | Kyousuke Mineo / Jun'ichirou Yamashita | Porsche 996 GT3-R | Team Taisan Cinecitta | 1:53.1370 |
| 34th | 5 | Haruki Kurosawa / Tetsuji Tamanaka | Vemac RD320R | Team Mach | 1:54.1260 |
| 35th | 10 | Masayuki Ueda / Masataka Kawaguchi | Ferrari F430 | Jim Gainer | 1:54.5520 |
| 36th | 360 | Atsushi Tanaka / Masahiro Matsunaga | Chevrolet Corvette Z06R | Tomei Sports | 1:56.8540 |
| 37th | 69 | Hiroki Yoshida / Melvin Choo | Mosler MT900M | Thunder Asia Racing | 1:56.9800 |