| 23 | Satoshi Motoyama / Michael Krumm | Nissan GT-R (R35) | Nismo | 1:43.6400 |
| 12 | Tsugio Matsuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:44.3310 |
| 32 | Ryou Michigami / Yuuki Nakayama | Honda HSV-010 GT (H010) | Nakajima Racing | 1:44.4350 |
| 39 | Juichi Wakisaka / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:44.6070 |
| 6 | Daisuke Itou / Kazuya Oshima | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:44.8630 |
| 36 | Kazuki Nakajima / Richard Lyons | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:45.0040 |
| 100 | Takuya Izawa / Naoki Yamamoto | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:45.0460 |
| 38 | Yuuji Tachikawa / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexus Team Zent Cerumo | 1:45.1700 |
| 1 | Masataka Yanagida / Ronnie Quintarelli | Nissan GT-R (R35) | Mola | 1:45.2190 |
| 18 | Takashi Kogure / Carlo van Dam | Honda HSV-010 GT (H010) | Weider Honda Racing | 1:45.3390 |
| 17 | Toshihiro Kaneishi / Koudai Tsukakoshi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:45.4130 |
| 19 | Seiji Ara / André Couto | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:45.4780 |
| 24 | Hironobu Yasuda / Björn Wirdheim | Nissan GT-R (R35) | Kondo Racing | 1:45.6040 |
| 8 | Ralph Firman / Takashi Kobayashi | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:46.3990 |
| 35 | Yuuji Kunimoto / Andrea Caldarelli | Lexus SC430 (UZZ40) | Lexus Team KeePer Kraft | 1:46.5590 |
| 87 | Kouji Yamanishi / Hideki Yamauchi | Lamborghini Gallardo LP600+ GT3 (09-7) | JLOC | 1:52.3760 |
| 11 | Tetsuya Tanaka / Katsuyuki Hiranaka | Audi R8 LMS ultra (AS42AOFGT3) | Gainer | 1:52.4010 |
| 15 | Tim Bergmeister / Takeshi Tsuchiya / Jörg Bergmeister | Porsche 997 GT3 R | Team ART Taste | 1:52.5820 |
| 3 | Yuuhi Sekiguchi / Katsumasa Chiyo | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:52.6730 |
| 43 | Shinichi Takagi / Kousuke Matsuura | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:53.2000 |
| 0 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:54.5400 |
| 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 1:54.6780 |
| 66 | Hiroki Yoshimoto / Kazuki Hoshino | Aston Martin V12 Vantage GT3 | A Speed | 1:54.9780 |
| 88 | Manabu Orido / Takayuki Aoki | Lamborghini Gallardo LP600+ GT3 (09-7) | JLOC | 1:55.0900 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:55.3190 |
| 52 | Hironori Takeuchi / Haruki Kurosawa | Mercedes-Benz SLS AMG GT3 | Green Tec & Leon With Shift | 1:56.5590 |
| 61 | Tetsuya Yamano / Kota Sasaki | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:56.9320 |
| 30 | Yuuki Iwasaki / Yuuya Sakamoto | Audi R8 LMS ultra (ABA-42BYHF) | Apr | 1:56.9690 |
| 360 | Atsushi Tanaka / Takuya Shirasaka | Callaway Corvette Z06R GT3 | Tomei Sports | 1:57.0090 |
| 911 | Kyousuke Mineo / Naoki Yokomizo | Porsche 997 GT3 R | Team Taisan Endless | 1:57.0900 |
| 48 | Hiroshi Takamori / Shogo Mitsuyama / Keiichi Inoue | Callaway Corvette Z06R GT3 | Dijon Racing | 1:57.8120 |
| 2 | Kazuho Takahashi / Hiroki Katou | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:57.9520 |
| 20 | Frank Yu / Hideki Noda / Kenji Kobayashi | Audi R8 LMS | Hitotsuyama Racing | 1:58.0270 |
| 22 | Hisashi Wada / Masaki Jounai | Vemac RD320R | R'Qs Motorsports | 1:58.5720 |
| 21 | Akihiro Tsuduki / Cyndie Allemann / Yukinori Taniguchi | Audi R8 LMS | Hitotsuyama Racing | 2:00.8300 |
| 86 | Jun'ichirou Yamashita / Hideshi Matsuda | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 2:02.2410 |
| 27 | Yutaka Yamagishi / Takuto Iguchi | Ferrari F430 GTC | LMP Motorsport | 2:02.7370 |
| 85 | Yuuya Sakamoto / Masaki Kano / Ryohei Sakaguchi | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 2:03.0230 |