The MP Motorsport driver shot up into P1 from P13 after heading out for a final flying lap after the third red flag.
Marcus Armstrong had been top of the timesheet for Hitech Grand Prix with a 1m41.050s, but after the third stoppage, opted not to head back on track.
But as he, Campos Racing’s Ralph Boschung and Liam Lawson (Carlin), who were running in P2 and P3 respectively, stayed in the garage, Drugovich took the chance to go quicker with a 1m40.422s putting him on pole for Sunday’s race.
Richard Verschoor slotted into P2 for Trident, with Jack Doohan in P3 with a 1m41.024s for Virtuosi Racing.
Their late laps knocked Armstrong, Boschung and Lawson into P4, P5 and P6, with a disappointed Armstrong watching from the pitwall as he was knocked off the top spot.
Jake Hughes will start on reverse-grid pole for Saturday’s sprint race, having finished in P10, with Juri Vips and Calan Williams in second and third.
Ayumu Iwasa was first to set a quick lap, putting in a 1m43.548s, before Ralph Boschung topped the timesheet after the first run of laps with a 1m42.096s.
Felipe Drugovich waited until after the rest of the field had completed their first lap to put in his time, going P2 with a 1m42.386s for MP Motorsport having topped practice earlier in the day.
He was knocked from the top spot as the times tumbled, with Van Amersfoort Racing’s Jake Hughes leading after 10 minutes having set a 1m41.538s.
The session was red-flagged with 18 minutes remaining after Theo Pourchaire’s ART Grand Prix-run car caught fire.
Smoke had been plummeting from the rear around the previous lap, before he stopped at the side of the track and the fire became visible.
It came after he ended up in the wall at Turn 24 during practice, prompting a red flag with eight minutes remaining and ending the session prematurely.
Ralph Boschung was set to improve on his time when running resumed around 15 minutes later, setting two green sectors and running 0.4s up.
But his attempt was thwarted when the red flag was waved again after Carlin’s Logan Sargeant hit the wall on the exit of Turn 17, returning the field to the pitlane with 12 minutes left on the clock.
Marcus Armstrong went quickest once running resumed, setting a 1m41.050s after going purple in sectors two and three.
Boschung had his lap once again thwarted as he was close to going top, narrowly avoiding a collision with ART’s Frederik Vesti at Turn 27 as the Mercedes junior prepared for a flying lap.
The Campos driver was forced to take avoiding action and missed out on the top spot by 0.007s. The incident will be investigated after the session.
There was a third red flag with five minutes remaining, but it appeared to be caused by a GPS alarm rather than an on track incident.
Enzo Fittipaldi could face a penalty after crossing the white line at the pit exit, while Amaury Cordeel is under investigation for not heeding the warning flags after Sargeant’s accident.
Marcus Armstrong is also under investigation after he was released into path of Jack Doohan in the pitlane on the second restart.
Cem Bolukbasi also crashed in practice at Turn 11, 20 minutes into running. The Charouz Racing System driver was taken to King Fahad Armed Forces Hospital for precautionary checks, and missed qualifying as a result.
2022 FIA F2 Saudia Arabia: Full qualifying result
| Cla | Driver | Team | Time | Gap |
|---|---|---|---|---|
| 1 |  Felipe Drugovich |  MP Motorsport | 1'40.422 | |
| 2 | Richard Verschoor |  Trident | 1'40.648 | 0.226 |
| 3 |  Jack Doohan | Virtuosi Racing | 1'41.024 | 0.602 |
| 4 |  Marcus Armstrong |  HitechGP | 1'41.050 | 0.628 |
| 5 |  Ralph Boschung |  Campos Racing | 1'41.057 | 0.635 |
| 6 | Liam Lawson | Carlin | 1'41.142 | 0.720 |
| 7 | Ayumu Iwasa |  Nissan e.Dams | 1'41.194 | 0.772 |
| 8 | Calan Williams | Trident | 1'41.469 | 1.047 |
| 9 |  Jüri Vips | HitechGP | 1'41.533 | 1.111 |
| 10 | Jake Hughes | Van Amersfoort Racing | 1'41.538 | 1.116 |
| 11 |  Dennis Hauger | Prema Powerteam | 1'41.710 | 1.288 |
| 12 | Clement Novalak | MP Motorsport | 1'41.710 | 1.288 |
| 13 |  Roy Nissany | Nissan e.Dams | 1'41.971 | 1.549 |
| 14 | Marino Sato | Virtuosi Racing | 1'42.178 | 1.756 |
| 15 |  Jehan Daruvala | Prema Powerteam | 1'42.181 | 1.759 |
| 16 | Enzo Fittipaldi |  Charouz Racing System | 1'42.520 | 2.098 |
| 17 |  Frederik Vesti |  ART Grand Prix | 1'42.905 | 2.483 |
| 18 | Olli Caldwell | Campos Racing | 1'43.120 | 2.698 |
| 19 |  Logan Sargeant | Carlin | 1'43.260 | 2.838 |
| 20 | Amaury Cordeel | Van Amersfoort Racing | 1'44.437 | 4.015 |
| 21 | Theo Pourchaire | ART Grand Prix | 1'44.736 | 4.314 |
| 22 |  Cem Bolukbasi | Charouz Racing System | ||
| View full results | ||||
