| 18 | Naoki Yamamoto / Frédéric Makowiecki | Honda HSV-010 GT (H010) | weider Modulo Dome Racing | 1:52.6940 |
| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:53.0400 |
| 38 | Yuuji Tachikawa / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexas Team Zent Cerumo | 1:53.0580 |
| 23 | Masataka Yanagida / Ronnie Quintarelli | Nissan GT-R (R35) | Nismo | 1:53.1010 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:53.2310 |
| 37 | Daisuke Itou / Andrea Caldarelli | Lexus SC430 (UZZ40) | Lexus Team KeePer Tom's | 1:53.3990 |
| 100 | Takuya Izawa / Takashi Kogure | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:53.4020 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:53.5660 |
| 1 | Satoshi Motoyama / Yuuhi Sekiguchi | Nissan GT-R (R35) | Mola | 1:53.7210 |
| 39 | Juichi Wakisaka / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:53.7860 |
| 12 | Tsugio Matsuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:54.1050 |
| 19 | Seiji Ara / André Couto | Lexus SC430 (UZZ40) | Lexus Team WedsSport Bandoh | 1:54.2500 |
| 24 | Hironobu Yasuda / Michael Krumm | Nissan GT-R (R35) | Kondo Racing | 1:54.2980 |
| 32 | Ryou Michigami / Daisuke Nakajima | Honda HSV-010 GT (H010) | Nakajima Racing | 1:54.5530 |
| 8 | Ralph Firman / Kousuke Matsuura | Honda HSV-010 GT (H010) | Autobacs Racing Team Aguri | 1:55.3690 |
| 61 | Tetsuya Yamano / Kota Sasaki / Takuto Iguchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 2:01.4810 |
| 3 | Kazuki Hoshino / Daiki Sasaki / Lucas Ordoñez | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:02.8710 |
| 52 | Hironori Takeuchi / Takeshi Tsuchiya / Naoya Gamou | Mercedes-Benz SLS AMG GT3 | Okinawa-Imp Racing With Shift | 2:03.1210 |
| 55 | Shinichi Takagi / Takashi Kobayashi / Tomoki Nojiri | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 2:03.2290 |
| 50 | Masaki Kano / Hideto Yasuoka / Ryohei Sakaguchi | Aston Martin V12 Vantage GT3 | Arnage Racing | 2:03.3320 |
| 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 2:03.4830 |
| 0 | Kyousuke Mineo / Naoki Yokomizo | Porsche 997 GT3 R | Team Taisan Ken Endless | 2:03.6050 |
| 86 | Kouji Yamanishi / Shin'ya Hosokawa / Yuuya Sakamoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 2:03.6300 |
| 21 | Akihiro Tsuduki / Richard Lyons | Audi R8 LMS | Hitotsuyama Racing | 2:03.7970 |
| 48 | Hiroshi Takamori / Katsumasa Chiyo / Masaki Tanaka | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 2:03.8070 |
| 62 | Haruki Kurosawa / Tsubasa Kurosawa / Akihiko Nakaya | Mercedes-Benz SLS AMG GT3 | Leon Racing | 2:03.8900 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 2:03.9110 |
| 9 | Shogo Mitsuyama / Yuu Yokomaku / Yuuya Sakamoto | Porsche 997 GT3 R | Pacific Direction Racing | 2:03.9130 |
| 16 | Hideki Mutou / Yuuki Nakayama | Honda CR-Z (ZF2) | Team Mugen | 2:03.9750 |
| 10 | Tetsuya Tanaka / Masayuki Ueda / Masataka Kawaguchi | Mercedes-Benz SLS AMG GT3 | Gainer | 2:04.1710 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 2:04.1730 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka / Jörg Müller | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 2:04.1930 |
| 30 | Yuuki Iwasaki / Igor Sushko / Kenji Kobayashi | Audi R8 LMS Ultra (ABA-42BYHF) | Apr | 2:04.2160 |
| 31 | Morio Nitta / Kouki Saga / Yuichi Nakayama | Toyota Prius (ZVW30) | Apr | 2:04.2680 |
| 2 | Kazuho Takahashi / Hiroki Katou / Carlo van Dam | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 2:04.6260 |
| 88 | Manabu Orido / Takayuki Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 2:05.4480 |
| 5 | Tetsuji Tamanaka / Jun'ichirou Yamashita / Naofumi Omoto | Nissan GT-R Nismo GT3 (R35) | Team Mach | 2:06.6230 |
| 87 | Hideki Yamauchi / Hiroki Yoshimoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 2:22.0330 |