| 12 | Tsugio Matsuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:55.6200 |
| 18 | Naoki Yamamoto / Frédéric Makowiecki | Honda HSV-010 GT (H010) | weider Modulo Dome Racing | 1:55.7090 |
| 38 | Yuji Tachikawa / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexas Team Zent Cerumo | 1:55.7780 |
| 1 | Satoshi Motoyama / Yuhi Sekiguchi | Nissan GT-R (R35) | Mola | 1:55.8440 |
| 100 | Takuya Izawa / Takashi Kogure | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:55.8860 |
| 39 | Juichi Wakisaka / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:56.0540 |
| 8 | Ralph Firman / Kousuke Matsuura | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:56.1850 |
| 37 | Daisuke Ito / Andrea Caldarelli | Lexus SC430 (UZZ40) | Lexus Team KeePer Tom's | 1:56.2140 |
| 23 | Masataka Yanagida / Ronnie Quintarelli | Nissan GT-R (R35) | Nismo | 1:56.3360 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:56.4680 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:56.5520 |
| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:56.5620 |
| 32 | Ryō Michigami / Daisuke Nakajima | Honda HSV-010 GT (H010) | Nakajima Racing | 1:56.6180 |
| 24 | Hironobu Yasuda / Michael Krumm | Nissan GT-R (R35) | Kondo Racing | 1:57.2450 |
| 19 | Seiji Ara / André Couto | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:57.4270 |
| 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 2:03.6740 |
| 16 | Hideki Mutou / Yuuki Nakayama | Honda CR-Z (ZF2) | Team Mugen | 2:04.2290 |
| 87 | Hideki Yamauchi / Hiroki Yoshimoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 2:04.3960 |
| 10 | Tetsuya Tanaka / Masayuki Ueda | Mercedes-Benz SLS AMG GT3 | Gainer | 2:04.6600 |
| 88 | Manabu Orido / Takayuki Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 2:04.6850 |
| 48 | Hiroshi Takamori / Katsumasa Chiyo | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:04.8760 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 2:05.1770 |
| 86 | Koji Yamanishi / Shin'ya Hosokawa | Lamborghini Gallardo GT3 (09-7) | JLOC | 2:05.2430 |
| 61 | Tetsuya Yamano / Kota Sasaki | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 2:05.2470 |
| 52 | Hironori Takeuchi / Takeshi Tsuchiya | Mercedes-Benz SLS AMG GT3 | Okinawa-Imp Racing With Shift | 2:05.2520 |
| 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 2:05.3030 |
| 0 | Kyousuke Mineo / Naoki Yokomizo | Porsche 997 GT3 R | Team Taisan Ken Endless | 2:05.3220 |
| 2 | Kazuho Takahashi / Hiroki Kato | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 2:05.3660 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 2:05.4700 |
| 62 | Haruki Kurosawa / Tsubasa Kurosawa | Mercedes-Benz SLS AMG GT3 | Leon Racing | 2:05.6010 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 2:05.6250 |
| 3 | Kazuki Hoshino / Daiki Sasaki | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:05.6390 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 2:06.3490 |
| 9 | Shogo Mitsuyama / Hisao Shigeta | Porsche 997 GT3 R | Pacific Direction Racing | 2:06.8070 |
| 5 | Tetsuji Tamanaka / Jun'ichirou Yamashita | Ferrari 458 Italia GT3 | Team Mach | 2:06.9430 |
| 360 | Takuya Shirasaka / Atsushi Tanaka | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 2:08.6620 |
| 30 | Yuuki Iwasaki / Igor Sushko | Audi R8 LMS Ultra (ABA-42BYHF) | Apr | 2:10.0430 |