Current points leader Cortese was on top for most of the final part of the qualifying battle. Kent was able to close right in, but moments after he did so, Cortese improved his pace to a 1m43.645s to take pole by 0.249 seconds, though Kent still claimed his first front row start at grand prix level.
Vinales was a pole contender for a while, but was pushed back to sixth as a big group of riders jumped up the order while following the Ajo team-mates around. The Avintia rider's final lap was not good enough to move him back towards the front, so he will start on the outside of row two.
Last year's Italian 125cc champion Niccolo Antonelli showed his best Moto3 form yet to take the final front row position for Gresini.
Veteran Hector Faubel (Aspar) and Niklas Ajo (TT Motion) were part of the pack chasing Cortese and Kent as they battled for pole, and that helped them jump from the midfield to fourth and fifth.
Behind Vinales, Alexis Masbou (Caretta), Miguel Oliveira (Monlau), Jakub Kornfeil (Ongetta) and title contender Luis Salom (RW) completed the top 10.
Jerez winner Romano Fenati was back in 17th for Team Italia, but just 0.916s off the pace in the very tight pack.