| 38 | Yuuji Tachikawa / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexas Team Zent Cerumo | 1:38.1740 |
| 23 | Masataka Yanagida / Ronnie Quintarelli | Nissan GT-R (R35) | Nismo | 1:38.2090 |
| 18 | Naoki Yamamoto / Frédéric Makowiecki | Honda HSV-010 GT (H010) | weider Modulo Dome Racing | 1:38.2200 |
| 1 | Satoshi Motoyama / Yuuhi Sekiguchi | Nissan GT-R (R35) | Mola | 1:38.3460 |
| 12 | Tsugio Matsuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:38.3850 |
| 100 | Takuya Izawa / Takashi Kogure | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:38.5660 |
| 37 | Daisuke Itou / Andrea Caldarelli | Lexus SC430 (UZZ40) | Lexus Team KeePer Tom's | 1:38.5730 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:38.6610 |
| 8 | Ralph Firman / Kousuke Matsuura | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:38.7250 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:38.8560 |
| 24 | Hironobu Yasuda / Michael Krumm | Nissan GT-R (R35) | Kondo Racing | 1:39.0120 |
| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:39.2270 |
| 39 | Juichi Wakisaka / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:39.5690 |
| 19 | Seiji Ara / André Couto | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:39.8930 |
| 32 | Ryou Michigami / Daisuke Nakajima | Honda HSV-010 GT (H010) | Nakajima Racing | 1:40.6060 |
| 3 | Kazuki Hoshino / Daiki Sasaki | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:47.2220 |
| 48 | Hiroshi Takamori / Katsumasa Chiyo | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:47.2360 |
| 50 | Masaki Kano / Hideto Yasuoka | Aston Martin V12 Vantage GT3 | Arnage Racing | 1:48.0360 |
| 61 | Tetsuya Yamano / Kota Sasaki | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:48.4080 |
| 30 | Yuuki Iwasaki / Igor Sushko | Nissan GT-R Nismo GT3 (R35) | Apr | 1:48.4160 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:48.5640 |
| 21 | Akihiro Tsuduki / Richard Lyons | Audi R8 LMS | Hitotsuyama Racing | 1:48.5710 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:48.9060 |
| 10 | Tetsuya Tanaka / Masayuki Ueda | Mercedes-Benz SLS AMG GT3 | Gainer | 1:49.2290 |
| 52 | Hironori Takeuchi / Takeshi Tsuchiya | Mercedes-Benz SLS AMG GT3 | Okinawa-Imp Racing With Shift | 1:49.2430 |
| 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 1:49.3630 |
| 87 | Hideki Yamauchi / Hiroki Yoshimoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:49.4230 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 1:49.4730 |
| 62 | Haruki Kurosawa / Tsubasa Kurosawa | Mercedes-Benz SLS AMG GT3 | Leon Racing | 1:49.5470 |
| 2 | Kazuho Takahashi / Hiroki Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:49.5570 |
| 16 | Hideki Mutou / Yuuki Nakayama | Honda CR-Z (ZF2) | Team Mugen | 1:49.6200 |
| 360 | Takuya Shirasaka / Atsushi Tanaka | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:49.7270 |
| 5 | Tetsuji Tamanaka / Jun'ichirou Yamashita | Nissan GT-R Nismo GT3 (R35) | Team Mach | 1:49.7540 |
| 86 | Kouji Yamanishi / Shin'ya Hosokawa | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:50.0320 |
| 88 | Manabu Orido / Takayuki Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:50.1250 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:50.4060 |
| 9 | Shogo Mitsuyama / Yuu Yokomaku | Porsche 997 GT3 R | Pacific Direction Racing | 1:51.3100 |
| 0 | Kyousuke Mineo / Naoki Yokomizo | Porsche 997 GT3 R | Team Taisan Ken Endless | 1:51.3520 |
| 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:51.4020 |