The Spaniard, quickest in all three practice sessions at Mugello, gained a massive four tenths of a second over his opponent as the chequered flag fell, making use of the slipstream from a gaggle of riders in front of him as he crossed the line.
Prior to that, it appeared traffic could be his downfall: several riders sitting up and spoiling quick laps for Vinales as they attempted to lock into his tow.
While the Avintia rider was forced to cut his way through the resulting traffic, Ajo man Cortese had a relatively clear track and went top with four minutes remaining, before lowering his benchmark next time around to a 1m58.587s.
Vinales was not to be denied however, and after a torrid weekend at the Sachsenring last week he duly sealed his fourth pole of the season.
Monlau's Alex Rins completes the front row for Sunday's race, with Efren Vazquez (Laglisse), Danny Kent (Ajo) and home favourite Niccolo Antonelli (Gresini) sixth. Fellow rising Italian star Romano Fenati took eighth for Team Italia, behind Ajo's Zulfahmi Khairuddin.
Laglisse rider Ivan Moreno crashed heavily at the first corner near the end of the session and had to be stretchered away.