Jorge Lorenzo took the early advantage as MotoGP's Assen weekend commenced with free practice on Thursday morning.
The Hondas had set the initial pace, but a mid-session 1m35.3s lap from Lorenzo put the Yamaha on top by 0.7 second. Lorenzo later improved to 1m35.263s, which kept him 0.35sec clear of the field as others improved.
A last-gasp lap from Tech 3's Cal Crutchlow made it a Yamaha one-two, the Briton demoting Honda's Marc Marquez to third just moments after the Spaniard had grabbed second.
Valentino Rossi was Lorenzo's closest rival for a long while and ended up fourth, ahead of championship leader and early pacesetter Dani Pedrosa's Honda.
Top CRT rider Aleix Espargaro took a remarkable sixth overall, beating satellite Honda men Stefan Bradl and Alvaro Bautista as well as all the Ducatis.
Michele Pirro, again riding the factory development bike under the Pramac banner in place of Ben Spies, was fastest Ducati in ninth, with works men Andrea Dovizioso and Nicky Hayden both outside the top 10.
Bradley Smith steadily worked his way up to 10th in his first ride since hand surgery to repair the damage caused in his Mugello crash.
Hiroshi Aoyama's stand-in Ivan Silva marked his return to MotoGP with the 23rd-fastest time.
Pos Rider Team/Bike Time Gap
1. Jorge Lorenzo Yamaha 1m35.263s
2. Cal Crutchlow Tech 3 Yamaha 1m35.613s + 0.350s
3. Marc Marquez Honda 1m35.883s + 0.620s
4. Valentino Rossi Yamaha 1m35.958s + 0.695s
5. Dani Pedrosa Honda 1m36.034s + 0.771s
6. Aleix Espargaro Aspar Aprilia 1m36.430s + 1.167s
7. Stefan Bradl LCR Honda 1m36.559s + 1.296s
8. Alvaro Bautista Gresini Honda 1m36.763s + 1.500s
9. Michele Pirro Pramac Ducati 1m36.910s + 1.647s
10. Bradley Smith Tech 3 Yamaha 1m37.002s + 1.739s
11. Andrea Dovizioso Ducati 1m37.041s + 1.778s
12. Nicky Hayden Ducati 1m37.153s + 1.890s
13. Karel Abraham Cardion Aprilia 1m37.346s + 2.083s
14. Hector Barbera Avintia FTR-Kawasaki 1m37.456s + 2.193s
15. Randy de Puniet Aspar Aprilia 1m37.489s + 2.226s
16. Andrea Iannone Pramac Ducati 1m37.538s + 2.275s
17. Danilo Petrucci Ioda-Suter-BMW 1m37.654s + 2.391s
18. Yonny Hernandez PBM Aprilia 1m37.917s + 2.654s
19. Colin Edwards Forward FTR-Kawasaki 1m38.147s + 2.884s
20. Claudio Corti Forward FTR-Kawasaki 1m38.334s + 3.071s
21. Michael Laverty PBM-Aprilia 1m38.874s + 3.611s
22. Bryan Staring Gresini FTR-Honda 1m39.708s + 4.445s
23. Ivan Silva Avintia FTR-Kawasaki 1m39.950s + 4.687s
24. Lukas Pesek Ioda-Suter-BMW 1m41.692s + 6.429s