The German's performance was all the more significant as his main title rival Maverick Vinales - currently 32 points behind Cortese - struggled with a water pump-related issue and wound up just 11th.
Running in dry conditions for the first time all weekend, times tumbled throughout the session and top spot traded hands on an almost constant basis.
That trend was halted moving into the final 10 minutes however as Cortese (Ajo KTM) hit the front.
Able to improve his own benchmark several times, the 22-year-old stayed clear of the chasing pack and eventually finished more than three tenths of a second clear.
There was no such luxury for Vinales. Forced to miss the opening half of the session due to a fluid leak on his Avintia FTR-Honda, he eventually got out onto the track but was on the back foot and never looked a contender.
In the end, he salvaged 11th with his final flyer, set just as the chequered flag flew.
In his absence, the second and third spots of the front row were claimed by Italian riders on Honda machinery, with Romano Fenati (Italia FMI) edging Niccolo Antonelli (Gresini) by just 0.019s.
Danny Kent (Ajo KTM) returned from an early fall to take fourth ahead of RW Kalex-KTM's Luis Salom, who trails Vinales by just 19 points.
One notable absentee was the Caretta Honda of Alexis Masbou. The French rider, currently sixth in the championship, was ruled out of the weekend and could well miss future races after fracturing his femur in testing at Misano.
Adrian Martin (Laglisse Honda) was also missing, having fractured his scaphoid earlier in the weekend.