Mitsunori Takaboshi set the day's benchmark time of 1m36.400s aboard the #3 NDDP Racing-branded Nissan Z he shares with Katsumasa Chiyo in the two-hour afternoon session, when conditions were at their best.
Sena Sakaguchi was second-fastest aboard the Yokohama-shod Racing Project Bandoh Toyota GR Supra with a time 0.168s slower, while the #23 NISMO car of Tsugio Matsuda made it a 1-3 for the Michelin Nissans, 0.217s off the pace.
Heavy rain in the morning session meant all the best times in the GT500 class were set in the afternoon, with Takaboshi going four seconds quicker than his teammate Chiyo had managed in the morning.
Fourth place for the Kondo Racing Nissan of Kohei Hirate meant the top four was monopolised by Michelin and Yokohama tyre users.
Bridgestone's top runner, the #37 TOM'S Toyota, was fifth-fastest and 1.543s off the pace in the hands of Ukyo Sasahara, despite the Japanese tyre firm having developed a new specification of wet tyre this off-season.
Two more Toyotas, the #36 TOM'S car (Ritomo Miyata) and the Rookie Racing (Kazuya Oshima) machine were next up, followed by the top Honda NSX-GT, the Team Kunimitsu machine of Tadasuke Makino.
However, Bridgestone did set the pace in the morning session when the weather was at its worst, as Kenta Yamashita beat the two Michelin-shod Nissans aboard the Rookie Toyota.
Running in a SUPER GT car for the first time since the crash at Suzuka in late January that left him with a compression fracture in his back, Yamashita set a best time of 1m40.533s, enough to beat the #23 Nissan of Ronnie Quintarelli by 0.234s.
Also making his return from injury was Kakunoshin Ota in the Nakajima Racing Honda. Ota set the car's best time of 1m39.676s in the afternoon, putting the team bottom of the GT500 order.
Setting the pace in the GT300 class was the Team Studie BMW M4 GT3, the sole car in the class on Michelin tyres.
Seiji Ara his best time of 1m44.502s in the afternoon in the car he is sharing with Masataka Yanagida, with full-season team-mate Bruno Spengler absent following his outing earlier this month at Okayama.
Two-time GT500 champion Yanagida is scheduled to share driving duties with Ara for both of SUPER GT's visits to Fuji this year.
Studie's nearest challengers for the top time were all Yokohama runners, led by the Team LeMans Audi R8 LMS GT3 in which third driver Seiya Jin set the best time of 1m44.740s. Third-fastest was another rookie in the form of Shun Koide aboard the Team UpGarage Honda NSX GT3.
The morning session was led by the Bridgestone-shod LEON Racing Mercedes AMG-GT3 of Naoya Gamou, who had set a benchmark of 1m48.912s in the slower conditions but was only 11th-fastest in the afternoon.
Despite the poor weather, there was only one red flag all day, which came when Togo Suganami crashed the Tsuchiya Engineering Toyota GR Supra GT exiting Turn 1 in the morning session.
The Tsuchiya Supra did not run in the afternoon as a result, and the team faces a tall order to repair the car for Sunday's running.
Fuji SUPER GT testing times (GT500 class):
| Pos. | No. | Team/Car | Drivers | Morning | Afternoon |
|---|---|---|---|---|---|
| 1 | 3 | NDDP Racing/Nissan |
|
1'40.986 | 1'36.400 |
| 2 | 19 | Racing Project Bandoh/Toyota |
|
1'48.894 | 1'36.568 |
| 3 | 23 | NISMO/Nissan |
|
1'40.767 | 1'36.617 |
| 4 | 24 | Kondo Racing/Nissan |
|
1'48.894 | 1'37.022 |
| 5 | 37 | TOM'S/Toyota |
|
1'42.625 | 1'37.943 |
| 6 | 36 | TOM'S/Toyota |
|
1'41.423 | 1'37.997 |
| 7 | 24 | Kondo Racing/Nissan |
|
1'40.533 | 1'37.999 |
| 8 | 100 | Kunimitsu/Honda |
|
1'43.147 | 1'38.016 |
| 9 | 8 | ARTA/Honda |
|
1'43.493 | 1'38.030 |
| 10 | 17 | Real Racing/Honda |
|
1'41.643 | 1'38.156 |
| 11 | 16 | ARTA/Honda |
|
1'42.919 | 1'38.217 |
| 12 | 1 | Impul/Nissan |
|
1'43.392 | 1'38.499 |
| 13 | 39 | SARD/Toyota |
|
1'42.448 | 1'38.535 |
| 14 | 38 | Cerumo/Toyota |
|
1'42.373 | 1'39.289 |
| 15 | 64 | Nakajima Racing/Honda |
|
1'45.955 | 1'39.676 |
Katsumasa Chiyo
Ronnie Quintarelli
Giuliano Alesi
Bertrand Baguette
