Despite the threat of a typhoon looming over Saturday's proceedings, the 45-minute FP2 got underway on time at 10.50am local time on a soaked track as teams opted not to modify the schedule.
After the first 10 minutes of running, Pramac Ducati’s Johann Zarco led the way with a 1m58.054s – though his stint at the top of the standings would be short-lived, the lead changing hands constantly as riders got a feel for the conditions.
When the red flag came out with just over 12 minutes remaining to clear up debris from a crash for Honda’s Pol Espargaro, his teammate Marquez led the way with a 1m55.232s.
Although Marquez initially held an advantage of close to a second over the field, Pramac Ducati’s Jorge Martin had whittled that down to just 0.144s prior to the brief stoppage.
When the session got back underway, Marquez’s benchmark would go unchallenged through to the chequered flag.
Martin remained second from Jack Miller, who leads the combined order after topping Friday's dry practice session for Ducati, and KTM’s Miguel Oliveira.
Zarco ended up fifth on the second Pramac Ducati, though faces Q1 after missing the top 10 by 0.001s following a crash in FP1.
Franco Morbidelli was the lead Yamaha rider in sixth ahead of Enea Bastianini (Gresini Ducati), Alex Marquez (LCR Honda) Luca Marini (VR46 Ducati) and Fabio Quartararo (Yamaha).
Bastianini is another rider who will have to face Q1 as a crash in FP1 has left him 14th in the combined order.
Aprilia's Aleix Espargaro ended FP2 in 11th but will go directly through to Q2 on the strength of his Friday time along with fellow title contenders Francesco Bagnaia, who was 15th for Ducati, and Quartararo.
Also with a free pass to Q2 are Honda duo Marquez and Pol Espargaro, KTM pair Oliveira and Brad Binder, Marini and the second Aprilia of Maverick Vinales, who was 18th-fastest on Saturday morning.
Binder was 24th-fastest following a crash, the South African sliding off his RC16 at Turn 3 just prior to the red flag.
MotoGP Japanese Grand Prix - FP2 results:
| Cla | # | Rider | Bike | Time | Gap |
|---|---|---|---|---|---|
| 1 | 93 |  Marc Marquez |
Honda | 1'55.232 | |
| 2 | 89 | Jorge Martin |
Ducati | 1'55.376 | 0.144 |
| 3 | 43 |  Jack Miller |
Ducati | 1'55.387 | 0.155 |
| 4 | 88 |  Miguel Oliveira |
KTM | 1'55.428 | 0.196 |
| 5 | 5 |  Johann Zarco |
Ducati | 1'55.630 | 0.398 |
| 6 | 21 |  Franco Morbidelli |
Yamaha | 1'56.168 | 0.936 |
| 7 | 23 | Enea Bastianini |
Ducati | 1'56.197 | 0.965 |
| 8 | 73 | Alex Marquez |
Honda | 1'56.349 | 1.117 |
| 9 | 10 | Luca Marini |
Ducati | 1'56.548 | 1.316 |
| 10 | 20 | Fabio Quartararo |
Yamaha | 1'56.561 | 1.329 |
| 11 | 41 | Aleix Espargaro |
Aprilia | 1'56.577 | 1.345 |
| 12 | 49 | Fabio Di Giannantonio |
Ducati | 1'56.588 | 1.356 |
| 13 | 72 | Marco Bezzecchi |
Ducati | 1'56.655 | 1.423 |
| 14 | 35 |  Cal Crutchlow |
Yamaha | 1'56.743 | 1.511 |
| 15 | 63 | Francesco Bagnaia |
Ducati | 1'56.752 | 1.520 |
| 16 | 87 | Remy Gardner |
KTM | 1'56.851 | 1.619 |
| 17 | 30 |  Takaaki Nakagami |
Honda | 1'56.874 | 1.642 |
| 18 | 12 | Maverick Viñales |
Aprilia | 1'56.925 | 1.693 |
| 19 | 44 | Pol Espargaro |
Honda | 1'57.003 | 1.771 |
| 20 | 25 | Raúl Fernández |
KTM | 1'57.292 | 2.060 |
| 21 | 40 |  Darryn Binder |
Yamaha | 1'57.606 | 2.374 |
| 22 | 45 | Tetsuta Nagashima |
Honda | 1'57.656 | 2.424 |
| 23 | 42 | Alex Rins |
Suzuki | 1'57.671 | 2.439 |
| 24 | 33 | Brad Binder |
KTM | 1'57.827 | 2.595 |
| 25 | 85 | Takuya Tsuda |
Suzuki | 1'58.631 | 3.399 |
| View full results | |||||
