Dani Pedrosa denied Yamaha a one-two as he snatched the top spot in the final seconds of third MotoGP practice at Sepang.
With rain in the air and some dampness on the track initially, Honda did not appear too fussed about chasing quick times at first, with Marc Marquez not even going for a flying lap until the last few minutes.
As the Hondas hung back, Yamaha led the way. Valentino Rossi was fastest for a long spell before Jorge Lorenzo pipped him by 0.093 seconds as both closed to within 0.4s of Pedrosa's Friday pace.
Pedrosa would not be denied, though, and on his final lap of the session did a 2m00.877s to beat Lorenzo by 0.046s.
Marquez was only seventh, a second off the pace.
Stefan Bradl's LCR Honda, Cal Crutchlow's Tech 3 Yamaha and Alvaro Bautista's Gresini Honda completed the top six.
The top five prototype teams secured the automatic Q2 places.
Leading CRT rider Aleix Espargaro did threaten to snatch a top 10 spot late on, but Bradley Smith improved enough to fend the Aspar man off.
Pos Rider Team/Bike Time Gap 1. Dani Pedrosa Honda 2m00.877s 2. Jorge Lorenzo Yamaha 2m00.923s +0.046s 3. Valentino Rossi Yamaha 2m00.970s +0.093s 4. Stefan Bradl LCR Honda 2m01.083s +0.206s 5. Cal Crutchlow Tech 3 Yamaha 2m01.373s +0.496s 6. Alvaro Bautista Gresini Honda 2m01.623s +0.746s 7. Marc Marquez Honda 2m01.956s +1.079s 8. Andrea Dovizioso Ducati 2m01.966s +1.089s 9. Nicky Hayden Ducati 2m02.226s +1.349s 10. Bradley Smith Tech 3 Yamaha 2m02.388s +1.511s 11. Aleix Espargaro Aspar Aprilia 2m02.555s +1.678s 12. Andrea Iannone Pramac Ducati 2m02.564s +1.687s 13. Hector Barbera Avintia FTR-Kawasaki 2m03.238s +2.361s 14. Yonny Hernandez Pramac Ducati 2m03.558s +2.681s 15. Hiroshi Aoyama Avintia FTR-Kawasaki 2m03.660s +2.783s 16. Randy de Puniet Aspar Aprilia 2m03.834s +2.957s 17. Claudio Corti Forward FTR-Kawasaki 2m03.879s +3.002s 18. Colin Edwards Forward FTR-Kawasaki 2m04.306s +3.429s 19. Danilo Petrucci Ioda-Suter-BMW 2m04.936s +4.059s 20. Luca Scassa Cardion Aprilia 2m05.227s +4.350s 21. Michael Laverty PBM Aprilia 2m05.358s +4.481s 22. Bryan Staring Gresini FTR-Honda 2m06.601s +5.724s 23. Damian Cudlin PBM-Aprilia 2m06.916s +6.039s 24. Lukas Pesek Ioda-Suter-BMW 2m06.946s +6.069s
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