Dani Pedrosa topped a drying MotoGP FP2 ahead of the Japanese Grand Prix by half a second from Scott Redding, while Andrea Dovizioso and Marc Marquez elected against running.
Rain during the lunch break left the Motegi circuit damp for the start of the second 45-minute MotoGP session of the weekend, with only 11 riders posting laptimes in the conditions.
Honda's Pedrosa set the early pace with a 1:58.637s, before Valentino Rossi guided his Yamaha to a 1:57.860s moments later.
The Italian was quickly deposed by Nieto Ducati's Karel Abraham by just under six hundredths, with Johann Zarco beginning his residence at the top of the timesheets with a 1:55.847s.
The Tech3 rider went on a run of session-best laps which culminated in a 1:54.417s, with Yamaha stablemate Maverick Vinales close to four tenths adrift in second.
Zarco further cemented his position at the top of the standings with a 1:53.728s with 10 minutes remaining, but Jack Miller would demote him with a 1:52.863s on his slick-fitted Pramac Ducati.
The Australian went on to post a 1:50.921s, with more riders venturing out on slicks in the latter stages for a few laps.
Miller raised the benchmark to a 1:49.022s in the closing stages, before Pramac teammate Danilo Petrucci edged ahead with a 1:48.939s.
A last-gasp effort from Pedrosa of 1:48.136s deposed the Italian, while Aprilia's Redding leaped up to second ahead of the Pramac pairing.
Zarco was shuffled back to fifth in the end ahead of Tech3 team-mate Hafizh Syahrin, while KTM's Bradley Smith, Avintia's Xavier Simeon, Marc VDS' Tom Luthi and Suzuki test rider Sylvain Guintoli completed the top 10.
The factory Yamaha pair of Rossi and Vinales were 14th and 15th at the chequered flag, while FP1 pacesetter Andrea Dovizioso and championship leader Marc Marquez opted against completing any laps.
The field was one-rider fewer this afternoon after Ducati's Jorge Lorenzo withdrew from the event due to the fractured left wrist he suffered in a crash in Thailand two weeks ago.
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