The MP Motorsport driver, who also claimed victory in Saturday's sprint race, charged through the field from 10th to snatch the lead on lap 27 before building a solid lead to the Australian.
It makes Drugovich the first driver in the modern F2 era to win both races in one weekend and extends his championship lead, with second-placed Pourchaire finishing the feature race in eighth.
Drugovich ran a longer first stint than Doohan, waiting until lap 17 to switch to the hard tyres, with the Virtuosi driver having stopped six laps earlier.
It worked in his favour, emerging in ninth place with many drivers in front having yet to stop or having had difficult stops, including Juri Vips and Pourchaire.
Despite Doohan having built up a 2.4s lead by lap 22, Drugovich maintained his strong pace before sweeping past the leader at Turn 1.
Drugovich faces a post-race investigation for a pit stop infringement.
Poleman Doohan took his first F2 podium in second, having endured a difficult start to the season with Frederik Vesti in third for ART Grand Prix.
Doohan got a great start off the line, with Vesti moving up to second after Vips was slow off the mark.
Dennis Hauger suffered contact early on after an incident with Olli Caldwell, with the Prema driver forced to pit for a new front wing, dropping him down the order and handing him a five second penalty.
The safety car was deployed on lap four after Prema's Jehan Daruvala became stranded on track, having been hit from behind by fellow Red Bull junior Ayumu Iwasa (DAMS).
Racing resumed on lap seven, with Vips among the first to pit for the hard compound tyres and suffering a slow stop after a problem with his front left wheel.
Logan Sargeant (Carlin) and Vesti were next to pit, while Doohan followed suit on lap 11, emerging in ninth with a 4.7s advantage over Drugovich.
Clement Novalak, running on the alternate strategy and starting on softs, took the lead after passing Enzo Fittipaldi on lap 21, with neither driver having stopped.
Drugovich passed Roy Nissany (DAMS) for fifth on lap 23, putting him closer to Doohan, who was running in third.
Doohan passed a yet-to-stop Marcus Armstrong on lap 24 before Drugovich also cleared the Hitech driver, putting the pair into the net lead and prompting the final fight for victory, with Drugovich taking the lead on lap 27.
Further back, having pitted, Novalak made it up to 10th, before passing Lawson and Pourchaire in quick succession to finish fifth.
Sargeant took fourth place, with Pourchaire in sixth and Fittipaldi, also on the alternate strategy, in seventh.
Lawson took eighth, with Armstrong and Calan Williams in ninth and 10th respectively.
Drugovich now leads the standings with 86 points, 26 clear of Pourchaire, heading into the fifth round in Monaco next weekend.
MP Motorsport lead the teams' championship with 108 points, with ART Grand Prix second on 85.
| Cla | Driver | Team | Gap |
|---|---|---|---|
| 1 |  Felipe Drugovich |  MP Motorsport | |
| 2 |  Jack Doohan | Virtuosi Racing | 5.600 |
| 3 |  Frederik Vesti |  ART Grand Prix | 23.100 |
| 4 |  Logan Sargeant |  Carlin | 24.700 |
| 5 |  Clement Novalak | MP Motorsport | 25.000 |
| 6 | Enzo Fittipaldi |  Charouz Racing System | 31.400 |
| 7 |  Marcus Armstrong | HitechGP | 32.100 |
| 8 | Theo Pourchaire | ART Grand Prix | 35.600 |
| 9 | Liam Lawson | Carlin | 37.100 |
| 10 |  Roy Nissany | DAMS | 37.200 |
| 11 | Calan Williams |  Trident | 38.700 |
| 12 | Ayumu Iwasa | DAMS | 54.800 |
| 13 |  Dennis Hauger | Prema Powerteam | 55.000 |
| 14 | Olli Caldwell |  Campos Racing | 56.500 |
| 15 | Amaury Cordeel | Van Amersfoort Racing | 59.600 |
| 16 | Jake Hughes | Van Amersfoort Racing | 1'03.300 |
| 17 |  Jüri Vips | HitechGP | 1'14.800 |
| 18 | Richard Verschoor | Trident | 1'20.000 |
| 19 |  Marino Sato | Virtuosi Racing | 1'30.500 |
| 20 |  Cem Bolukbasi | Charouz Racing System | 1'33.800 |
 Jehan Daruvala | Prema Powerteam | ||
| View full results | |||
