| 39 | Juichi Wakisaka / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:31.9770 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:32.0150 |
| 12 | Tsugio Matsuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:32.0450 |
| 38 | Yuuji Tachikawa / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexas Team Zent Cerumo | 1:32.1980 |
| 1 | Satoshi Motoyama / Yuuhi Sekiguchi | Nissan GT-R (R35) | Mola | 1:32.2260 |
| 23 | Masataka Yanagida / Ronnie Quintarelli | Nissan GT-R (R35) | Nismo | 1:32.2870 |
| 18 | Naoki Yamamoto / Frédéric Makowiecki | Honda HSV-010 GT (H010) | weider Modulo Dome Racing | 1:32.2890 |
| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:32.3170 |
| 100 | Takuya Izawa / Takashi Kogure | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:32.3870 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:32.5700 |
| 8 | Ralph Firman / Kousuke Matsuura | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:32.5790 |
| 19 | Seiji Ara / André Couto | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:32.6070 |
| 24 | Hironobu Yasuda / Michael Krumm | Nissan GT-R (R35) | Kondo Racing | 1:32.7350 |
| 32 | Ryou Michigami / Daisuke Nakajima | Honda HSV-010 GT (H010) | Nakajima Racing | 1:33.2390 |
| 3 | Kazuki Hoshino / Daiki Sasaki | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:38.8330 |
| 48 | Hiroshi Takamori / Katsumasa Chiyo | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:38.8790 |
| 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 1:38.9200 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:39.0570 |
| 0 | Kyousuke Mineo / Naoki Yokomizo | Porsche 997 GT3 R | Team Taisan Ken Endless | 1:39.1370 |
| 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:39.2080 |
| 86 | Kouji Yamanishi / Shin'ya Hosokawa / Yuuya Sakamoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:39.3230 |
| 9 | Shogo Mitsuyama / Yuu Yokomaku | Porsche 997 GT3 R | Pacific Direction Racing | 1:39.4140 |
| 52 | Hironori Takeuchi / Takeshi Tsuchiya | Mercedes-Benz SLS AMG GT3 | Okinawa-Imp Racing With Shift | 1:39.4640 |
| 61 | Tetsuya Yamano / Kota Sasaki | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:39.5920 |
| 2 | Kazuho Takahashi / Hiroki Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:39.6420 |
| 16 | Hideki Mutou / Yuuki Nakayama | Honda CR-Z (ZF2) | Team Mugen | 1:39.6440 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:39.6570 |
| 21 | Akihiro Tsuduki / Richard Lyons | Audi R8 LMS | Hitotsuyama Racing | 1:39.7130 |
| 88 | Manabu Orido / Takayuki Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:39.8130 |
| 62 | Haruki Kurosawa / Masanobu Katou | Mercedes-Benz SLS AMG GT3 | Leon Racing | 1:40.0740 |
| 87 | Hideki Yamauchi / Hiroki Yoshimoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:40.1690 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:40.2330 |
| 10 | Tetsuya Tanaka / Masayuki Ueda | Mercedes-Benz SLS AMG GT3 | Gainer | 1:40.3850 |
| 50 | Masaki Kano / Hideto Yasuoka / Ryohei Sakaguchi | Aston Martin V12 Vantage GT3 | Arnage Racing | 1:40.5090 |
| 5 | Tetsuji Tamanaka / Jun'ichirou Yamashita / Naofumi Omoto | Ferrari 458 Italia GT3 | Team Mach | 1:40.7890 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 1:40.8240 |
| 30 | Yuuki Iwasaki / Fairuz Fauzy / Kenji Kobayashi | Audi R8 LMS Ultra (ABA-42BYHF) | Apr | 1:40.8380 |
| 360 | Takuya Shirasaka / Atsushi Tanaka | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:41.0740 |
| 7 | Igor Sushko / Yuuji Ide | Nissan GT-R Nismo GT3 (R35) | Bonds Racing | 1:41.6680 |
| 96 | Masaki Tanaka / Keiichi Inoue | Callaway Corvette Z06R GT3 | Tomei Sports | 1:43.3360 |