Dani Pedrosa edged out MotoGP championship leader Jorge Lorenzo by just over one tenth of a second in the penultimate practice session at Motegi.
It had been Lorenzo who set the pace early on, building on his chart-topping practice one form by dropping down to a 1m46.392s - at the time the fastest lap of the weekend.
As the Yamaha man was flying, Pedrosa looked to be struggling, lapping more than six tenths of a second slower and also suffering an off-track moment.
With 30 minutes to run however the Spaniard suddenly found massive gains, closing to within 0.123s of Lorenzo before jumping to the top of the timesheets with his next lap.
Lorenzo would respond in the final two minutes, improving the benchmark by one hundredth of a second, only for Pedrosa to once again go faster with a 1m46.088s in the final two minutes.
In a mirror of the championship situation, the pair were in a class of their own for most of the session.
That changed in the final minutes, when Andrea Dovizioso, Stefan Bradl and Valentino Rossi were among those to make massive improvements.
Dovizioso's was the most significant, the Tech 3 rider closing to within 0.2s of Pedrosa.
LCR Honda's Bradl meanwhile did enough to snatch fourth from Rossi. The Italian had gone third with four minutes to run, but as others also improved he eventually slipped to fifth.
That still put him ahead of the second works Yamaha and Honda of Ben Spies and Casey Stoner, the pair finishing sixth and seventh respectively.
Gresini's Alvaro Bautista claimed eighth ahead of Cal Crutchlow (Tech 3), Nicky Hayden (Ducati) and Yamaha wildcard entry Katsuyuki Nakasuga.
Pos Rider Team/Bike Time Gap
1. Dani Pedrosa Honda 1m46.088s
2. Jorge Lorenzo Yamaha 1m46.190s + 0.102s
3. Andrea Dovizioso Tech 3 Yamaha 1m46.282s + 0.194s
4. Stefan Bradl LCR Honda 1m46.428s + 0.340s
5. Valentino Rossi Ducati 1m46.687s + 0.599s
6. Ben Spies Yamaha 1m46.912s + 0.824s
7. Casey Stoner Honda 1m46.978s + 0.890s
8. Alvaro Bautista Gresini Honda 1m46.983s + 0.895s
9. Cal Crutchlow Tech 3 Yamaha 1m46.984s + 0.896s
10. Nicky Hayden Ducati 1m47.592s + 1.504s
11. Katsuyuki Nakasuga Yamaha 1m47.801s + 1.713s
12. Hector Barbera Pramac Ducati 1m48.232s + 2.144s
13. Aleix Espargaro Aspar Aprilia 1m48.470s + 2.382s
14. Karel Abraham Cardion Ducati 1m48.757s + 2.669s
15. Randy de Puniet Aspar Aprilia 1m48.770s + 2.682s
16. Colin Edwards Forward Suter-BMW 1m49.539s + 3.451s
17. James Ellison Paul Bird Aprilia 1m49.652s + 3.564s
18. Michele Pirro Gresini FTR-Honda 1m49.770s + 3.682s
19. Roberto Rolfo Speed Master Aprilia 1m50.292s + 4.204s
20. Yonny Hernandez Avintia FTR-Kawasaki 1m50.333s + 4.245s
21. Ivan Silva Avintia FTR-Kawasaki 1m50.924s + 4.836s
22. Danilo Petrucci Ioda Suter-BMW 1m51.270s + 5.182s