The Trident driver grabbed the top spot by just two-hundredths of a second from the Australian, who is embroiled in a tight title fight with Prema’s Dennis Hauger.
The top 10 was covered by just 0.2 seconds in a session interrupted by a red flag and plagued by the usual slow lap congestion.
Doohan, who sits second in the drivers championship, finished in second, while Johnathan Hoggard took his best ever grid position for Jenzer Motorsport by finishing in third.
Frederik Vesti of ART finished fourth, just 0.07s slower than Novalak, with team-mate Juan Manuel Correa in fifth. Championship leader Dennis Hauger only managed eighth place.
Roman Stanek will start on pole for the first sprint race for Hitech Grand Prix, which will now take place this afternoon instead of tomorrow morning because of poor weather forecast at the track.
Victor Martins (MP Motorsport) will start alongside him, with Logan Sargeant of Charouz Racing System and Jak Crawford of Hitech on the second row.
Jack Doohan was first out on track again, as he was in this morning’s practice session.
Heavy traffic while drivers attempted to create space caused frustration, with Clement Novalak telling his team it was “crazy.”
Frederik Vesti, ART Grand Prix
Photo by: James Gasperotti / Motorsport Images
Doohan managed to break clear of the pack to take a flying lap, but struggled with grip, complaining of oversteer, and went wide at the exit of turn 10 before almost losing his lap time for track limits at the last corner.
Seven minutes into the session, the red flag was waved after Jonny Edgar found the wall in sector three, crashing into the barriers and ending his session.
Caio Collet had topped the time sheet before the stoppage, while Arthur Leclerc sat P2, with Hauger and Doohan slotted into P3 and P4 respectively.
The session resumed less than 10 minutes later, with most drivers continuing on the hard tyres they had started the session with.
Doohan quickly took the top of the timesheet, setting a 1m54.927s, almost 0.2s ahead of Collet.
Hauger was lucky to keep his Prema-sponsored car out of the wall after running wide in the middle of the lap while also struggling with his tyres, but only managed P13.
Victor Martins narrowly avoided contact with Ayrton Simmons into Turn 4 in an incident set to be investigated by the stewards after the session.
Much of the field pitted for a second set of hard tyres around the halfway point, before re-emerging for the last 10 minutes of the session.
Tijmen van der Helm was forced to pit with seven minutes remaining after suffering front wing damage, but was the only car affected.
With five minutes to go, Doohan’s fresh tyres allowed him to beat his previous time by almost two-and-a-half-tenths, setting a 1m54.677s, with Johnathan Hoggard in second place just one-hundredth behind him.
The usual traffic chaos ensued as the drivers stacked up for their final flying laps, with Doohan sending it down the inside at one point in a move more akin to something seen in race conditions.
But Novalak snatched pole from his team-mate in the last 30 seconds with a mighty final lap, taking his first front-row start in the series.