| 36 | Kazuki Nakajima / Yuuhi Sekiguchi | Lexus LC500 (URZ100) | Lexus Team au Tom's | 1:10.281 |
| 64 | Narain Karthikeyan / Tadasuke Makino | Honda NSX-GT (NC1) | Modulo Nakajima Racing | 1:10.508 |
| 17 | Koudai Tsukakoshi / Bertrand Baguette | Honda NSX-GT (NC1) | Keihin Real Racing | 1:10.535 |
| 37 | Ryou Hirakawa / Nick Cassidy | Lexus LC500 (URZ100) | Lexus Team KeePer Tom's | 1:10.568 |
| 3 | Kouhei Hirate / Frédéric Makowiecki | Nissan GT-R (R35) | NDDP Racing with B-Max | 1:10.581 |
| 1 | Naoki Yamamoto / Jenson Button | Honda NSX-GT (NC1) | Team Kunimitsu | 1:10.623 |
| 6 | Kazuya Ooshima / Kenta Yamashita | Lexus LC500 (URZ100) | Lexus Team Le Mans Wako's | 1:10.638 |
| 19 | Yuuji Kunimoto / Syou Tsuboi | Lexus LC500 (URZ100) | Lexus Team WedsSport Bandoh | 1:10.650 |
| 8 | Tomoki Nojiri / Takuya Izawa | Honda NSX-GT (NC1) | ARTA | 1:10.845 |
| 23 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | NISMO | 1:10.881 |
| 38 | Yuuji Tachikawa / Hiroaki Ishiura | Lexus LC500 (URZ100) | Lexus Team Zent Cerumo | 1:10.999 |
| 24 | Mitsunori Takaboshi / Jann Mardenborough | Nissan GT-R (R35) | Kondo Racing | 1:11.117 |
| 16 | Hideki Mutou / Daisuke Nakajima | Honda NSX-GT (NC1) | Team Mugen | 1:11.208 |
| 12 | Daiki Sasaki / James Rossiter | Nissan GT-R (R35) | Team Impul | 1:11.426 |
| 39 | Heikki Kovalainen / Yuuichi Nakayama | Lexus LC500 (URZ100) | Lexus Team SARD | 1:11.894 |
| 720 | Seiji Ara / Alex Palou | McLaren 720S (PA1) | McLaren Customer Racing Japan | 1:18.124 |
| 34 | Ryou Michigami / Hiroki Ootsu | Honda NSX-GT3 (NC1) | Modulo Drago Corse | 1:18.181 |
| 55 | Shin'ichi Takagi / Nirei Fukuzumi | Honda NSX-GT3 (NC1) | ARTA | 1:18.341 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | Mercedes-AMG GT3 (C190) | Goodsmile Racing & Team Ukyo | 1:18.357 |
| 25 | Takamitsu Matsui / Kimiya Satou | Toyota 86MC (ZN6) | Tsuchiya Engineering | 1:18.404 |
| 61 | Takuto Iguchi / Hideki Yamauchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:18.487 |
| 35 | Nattapong Hortongkum / Sean Walkinshaw | Lexus RC F GT3 (USC10) | Panther Arto Team Thailand | 1:18.563 |
| 56 | Kazuki Hiramine / Sacha Fenestraz | Nissan GT-R Nismo GT3 (R35) | Kondo Racing | 1:18.655 |
| 60 | Hiroki Yoshimoto / Ritomo Miyata | Lexus RC F GT3 (USC10) | LM Corsa | 1:18.678 |
| 7 | Tomonobu Fujii / Joao Paolo de Oliveira | Aston Martin Vantage GT3 (ABA-AM601) | D'station Racing AMR | 1:18.730 |
| 360 | Takayuki Aoki / Yuusaku Shibata | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:18.757 |
| 31 | Kouki Saga / Yuuki Nakayama | Toyota Prius (ZVW52) | Apr | 1:18.788 |
| 10 | Kazuki Hoshino / Keishi Ishikawa | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:18.830 |
| 33 | Shaun Thong / Shinya Michimi | Nissan GT-R Nismo GT3 (R35) | X Works | 1:18.864 |
| 65 | Naoya Gamou / Tougo Suganami | Mercedes-AMG GT3 (C190) | K2 R&D Leon Racing | 1:18.944 |
| 96 | Morio Nitta / Sena Sakaguchi | Lexus RC F GT3 (USC10) | K-tunes Racing | 1:18.991 |
| 18 | Takashi Kobayashi / Kousuke Matsuura | Honda NSX-GT3 (NC1) | Team Upgarage | 1:19.023 |
| 21 | Richard Lyons / Ryuichiro Tomita | Audi R8 LMS (ABA-4SCSPD) | Audi Team Hitotsuyama | 1:19.108 |
| 30 | Hiroaki Nagai / Manabu Orido | Toyota Prius (ZVW52) | Apr | 1:19.159 |
| 52 | Shigekazu Wakisaka / Hiroki Yoshida | Toyota Mark X (GRX133) | Saitama Toyopet Green Brave | 1:19.173 |
| 88 | Takashi Kogure / Yuuya Motojima | Lamborghini Huracan GT3 (ALSCGT2015) | JLOC | 1:19.180 |
| 11 | Katsuyuki Hiranaka / Hironobu Yasuda | Nissan GT-R Nismo GT3 (R35) | Gainer | 1:19.209 |
| 87 | Tsubasa Takahashi / André Couto | Lamborghini Huracan GT3 (ALSCGT2015) | JLOC | 1:19.446 |
| 9 | Naoki Yokomizo / Kyousuke Mineo | Porsche 991 GT3 R | Pacific Racing with Good Speed | 1:19.586 |
| 5 | Natsu Sakaguchi / Yuuya Hiraki | Toyota 86MC (ZN6) | Team Mach | 1:19.587 |
| 48 | Masaki Tanaka / Taiyou Iida | Nissan GT-R Nismo GT3 (R35) | Nilzz Racing | 1:20.194 |
| 2 | Kazuho Takahashi / Hiroki Katou | Lotus Evora (122) | Cars Tokai Dream28 | 1:20.264 |
| 50 | Masaki Kanou / Ryousei Yamashita | Mercedes-AMG GT3 (C190) | Arnage Racing | 1:20.452 |