| 23 | Masataka Yanagida / Ronnie Quintarelli | Nissan GT-R (R35) | Nismo | 1:35.3730 |
| 32 | Ryou Michigami / Daisuke Nakajima | Honda HSV-010 GT (H010) | Nakajima Racing | 1:35.9970 |
| 24 | Hironobu Yasuda / Michael Krumm | Nissan GT-R (R35) | Kondo Racing | 1:36.4900 |
| 19 | Seiji Ara / André Couto | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:36.6000 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:36.6400 |
| 100 | Takuya Izawa / Takashi Kogure | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:36.7840 |
| 12 | Tsugio Matsuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:37.1090 |
| 8 | Ralph Firman / Kousuke Matsuura | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:37.2030 |
| 18 | Naoki Yamamoto / Frédéric Makowiecki | Honda HSV-010 GT (H010) | weider Modulo Dome Racing | 1:37.2110 |
| 37 | Daisuke Itou / Andrea Caldarelli | Lexus SC430 (UZZ40) | Lexus Team KeePer Tom's | 1:37.4220 |
| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:38.0390 |
| 38 | Yuuji Tachikawa / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexas Team Zent Cerumo | 1:38.0760 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:39.4530 |
| 0 | Kyousuke Mineo / Naoki Yokomizo | Porsche 997 GT3 R | Team Taisan Ken Endless | 1:44.9570 |
| 48 | Hiroshi Takamori / Katsumasa Chiyo | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:45.1980 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:45.4650 |
| 3 | Kazuki Hoshino / Daiki Sasaki | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:46.3600 |
| 87 | Hideki Yamauchi / Hiroki Yoshimoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:47.3500 |
| 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 1:47.4630 |
| 10 | Tetsuya Tanaka / Masayuki Ueda | Mercedes-Benz SLS AMG GT3 | Gainer | 1:48.0670 |
| 52 | Hironori Takeuchi / Takeshi Tsuchiya | Mercedes-Benz SLS AMG GT3 | Okinawa-Imp Racing With Shift | 1:48.4750 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:48.5210 |
| 50 | Masaki Kano / Hideto Yasuoka | Aston Martin V12 Vantage GT3 | Arnage Racing | 1:48.5280 |
| 62 | Haruki Kurosawa / Masanobu Katou | Mercedes-Benz SLS AMG GT3 | Leon Racing | 1:49.1620 |
| 2 | Kazuho Takahashi / Hiroki Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:49.3740 |
| 61 | Tetsuya Yamano / Kota Sasaki | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:49.5440 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:49.7780 |
| 9 | Shogo Mitsuyama / Yuu Yokomaku | Porsche 997 GT3 R | Pacific Direction Racing | 1:52.1810 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 1:52.7250 |
| 7 | Igor Sushko / Ryou Orime | Nissan GT-R Nismo GT3 (R35) | Bonds Racing | 1:52.7380 |
| 21 | Akihiro Tsuduki / Richard Lyons | Audi R8 LMS | Hitotsuyama Racing | 1:53.2760 |
| 5 | Tetsuji Tamanaka / Jun'ichirou Yamashita | Ferrari 458 Italia GT3 | Team Mach | 1:53.3170 |
| 16 | Hideki Mutou / Yuuki Nakayama | Honda CR-Z (ZF2) | Team Mugen | 1:54.0300 |
| 360 | Takuya Shirasaka / Atsushi Tanaka | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:58.3760 |