Johann Zarco will start at the front of the grid in Assen on Sunday courtesy of a rapid final lap on Saturday after battling it out with Marc Marquez in a wet qualifying session.
The Monster Yamaha Tech 3 rider clocked one minute 46.141 seconds to become the first Frenchman for 15 years to claim pole in the premier class.
Defending champion Marquez (Repsol Honda) was 0.065 off the pace, having looked set to be quickest on a damp day in the Netherlands.
Danilo Petrucci followed up his first front row start in the Catalan GP by taking third spot for Octo Pramac Racing.
Valentino Rossi will start the ninth race of the season in fourth spot, while Scott Redding and Jonas Folger completing the second row.
Championship leader Maverick Vinales could only qualify in 11th spot, two places back from Andrea Dovizioso – his nearest rival in the battle for the title.
1. Johann Zarco (Monster Yamaha Tech 3) 1:46.141
2. Marc Marquez (Repsol Honda) 1:46.206
3. Danilo Petrucci (Pramac) 1:46.526
4. Valentino Rossi (Movistar Yamaha MotoGP) 1:46.705
5. Scott Redding (OCTO Pramac Racing) 1:47.574
6. Jonas Folger (Monster Yamaha Tech 3) 1:47.663
7. Alvaro Bautista (Aspar Team) 1:47.663
8. Cal Crutchclow (LCR Honda) 1:48.042
9. Andrea Dovizioso (Ducati) 1:48.079
10. Sam Lowes (Aprilia) 1:48.121