Dani Pedrosa became the first rider to dip below the 1m46s mark to set the pace in the final MotoGP practice session at Motegi.
As had been the case in both Friday sessions top spot was effectively the exclusive domain of Pedrosa and his title rival Jorge Lorenzo, with the latter leading early on.
With 20 minutes to run however Pedrosa shaved more than three tenths of a second off his own best to drop down to a 1m45.792s.
Lorenzo's response never materialised, the Yamaha man finishing just over two tenths of a second down.
His works team-mate Ben Spies was third, less than a tenth of a second down the road.
Andrea Dovizioso made it three Yamahas in the top four, although Gresini's Alvaro Bautista was able to split the Italian and his Tech 3 stable-mate Cal Crutchlow.
Casey Stoner, hampered by his injuries yesterday, came home seventh, within seven tenths of team-mate Pedrosa.
Valentino Rossi meanwhile was the last man to finish within one second of the ultimate pace.
Ducati team-mate Nicky Hayden was 10th, behind LCR Honda's Stefan Bradl.
An impressive late rally carried CRT rider Aleix Espargaro (Aspar) up to 11th, ahead of Pramac Ducati satellite rider Hector Barbera and Yamaha wildcard entrant Katsuyuki Nakasuga.
Pos Rider Team/Bike Time Gap
1. Dani Pedrosa Honda 1m45.792s
2. Jorge Lorenzo Yamaha 1m46.057s + 0.265s
3. Ben Spies Yamaha 1m46.138s + 0.346s
4. Andrea Dovizioso Tech 3 Yamaha 1m46.220s + 0.428s
5. Alvaro Bautista Gresini Honda 1m46.354s + 0.562s
6. Cal Crutchlow Tech 3 Yamaha 1m46.436s + 0.644s
7. Casey Stoner Honda 1m46.480s + 0.688s
8. Valentino Rossi Ducati 1m46.641s + 0.849s
9. Stefan Bradl LCR Honda 1m47.028s + 1.236s
10. Nicky Hayden Ducati 1m47.240s + 1.448s
11. Aleix Espargaro Aspar Aprilia 1m47.685s + 1.893s
12. Hector Barbera Pramac Ducati 1m47.726s + 1.934s
13. Katsuyuki Nakasuga Yamaha 1m47.737s + 1.945s
14. Karel Abraham Cardion Ducati 1m47.791s + 1.999s
15. Randy de Puniet Aspar Aprilia 1m48.358s + 2.566s
16. James Ellison Paul Bird Aprilia 1m48.628s + 2.836s
17. Danilo Petrucci Ioda Suter-BMW 1m49.243s + 3.451s
18. Michele Pirro Gresini FTR-Honda 1m49.349s + 3.557s
19. Roberto Rolfo Speed Master Aprilia 1m49.353s + 3.561s
20. Yonny Hernandez Avintia FTR-Kawasaki 1m49.502s + 3.710s
21. Colin Edwards Forward Suter-BMW 1m49.974s + 4.182s
22. Ivan Silva Avintia FTR-Kawasaki 1m50.117s + 4.325s