The Gresini rider set the best ever lap of the Assen track as the riders entered the final very busy five minutes of the session and with the other riders all tangling for track space the time stood as a flurry of late fast laps went awry in the closing stages.
Honda's ecstatic wheelie-popping Italian will be hunting again for his first ever race win on Saturday, and is championship leader Danny Kent's closest rival in second overall.
Second on the grid goes to the ever improving rookie Jorge Navarro who had incredible speed over the closing turns of the track to save his final lap and move onto the front row for the Estrella Galicia 0,0 team.
Third went to Red Bull KTM Ajo rider Karel Hanika, who is starting to red iscover the form that was expected from him when he graduated from the Red Bull Rookies. It is the Czech rider's first front row start, achieved with his eighth lap which had previously topped the timesheets.
Navarro's speedy final attempt pushed Danny Kent down to fourth. The Leopard Racing rider had lead all of the previous sessions in the run up to qualifying but lacked pace in the final sector.
The British rider remained relaxed and positive heading into the race with a huge 51 point lead after spending the first half of the session doing long runs testing his race pace.
Husqvarna rider Isaac Vinales lines up fifth for the Laglisse team after engineering some great tows from his timed runs, with the Red Bull Ajo bike of Miguel Oliveira also lining up on row two in sixth.
Fabio Quartararo put in a string of fast laps, but was frustrated by riders looking to follow and traffic on the track in general and lines up in seventh on the second of the Estrella Gal icia 0,0 entries.
Romano Fenati, who had been Kent's main challenger in the morning practice starts eighth for Sky Racing Team VR46 and Leopard Racing's Efren Vazquez ninth, with all the top ten riders within a second of the top time and under the original lap record set last year.
The final place in the top ten went to Francesco Bagnaia, despite a late crash for the Mapfre Team Mahindra rider after being pushed wide.
Niccolo Antonelli was the first faller, his bobbling Ongetta-Rivacold bike entering the gravel just six minutes into the session. Running ninth at the time he then saw his lap time removed leaving him with no time set and his bike in the pits for repairs.
The Italian returned to the track with just seven minutes left, banging his crooked handlebar back into place as he left the pits. His first lap saw him move up to 25th before improving again to finish his qualifying session in a hard earned 19th.
Female rider Maria Herrera continued to g row in confidence and secured a 13th place start for the Husqvarna Factory Laglisse Team.
The SaxoPrint-RTG team continued to struggle for position and are looking to make up half a second on the straight and will be looking to improve in the race. Alexis Masbou starts 21st and Britain's John McPhee 23rd.
Assen features wild-card rides for Dutch rider Jorel Boerboom (FPW Racing) and Germany's Kevin Hanus, who start from the back of the grid in 35th and 36th respectively.
