The Virtuosi driver started 11th for Sunday’s race, lining up on the medium-compound tyres to run the alternative strategy.
He made steady progress in the early stages, running ninth before the first safety car.
But a well-timed pitstop under the second safety car meant he rejoined in second, behind Pourchaire.
He finally took the lead two laps from the end on the Kemmel Straight, and despite a close moment between the pair at Les Combes, made it home to repeat his win in Hungary last weekend, with Enzo Fittipaldi third for Rodin Carlin.
Pourchaire’s second-place finish returns him to the top of the standings after title rival Frederik Vesti (Prema) crashed on the way to the grid, leaving him unable to start the race.
Pourchaire now leads by 12 points with three rounds remaining, with Vesti in second and DAMS driver Ayumu Iwasa in third on 134 points.
Doohan’s win moves him 10 points ahead of Victor Martins (ART) in fourth.
With both Vesti and Martins spinning on the way to the grid, the start was delayed by five minutes, though the Frenchman escaped with no damage.
The gap left by his team-mate gave poleman Ollie Bearman (Prema) a solid advantage off the line, with Pourchaire slotting into second ahead of Rodin Carlin duo Zane Maloney and Fittipaldi.
The safety car was almost immediately deployed after contact between Iwasa and Dennis Hauger (MP Motorsport) at Les Combes, the former suffering terminal suspension damage.
Hauger was push-started by the marshals and later shown the black flag and disqualified for having been helped.
Racing resumed on lap four, with Maloney and Fittipaldi tussling for third. The Brazilian emerged ahead, with Martins capitalising to take fourth.
Further back, Arthur Leclerc's DAMS was spun by PHM driver Roy Nissany at Eau Rouge, his tyre later popping off, while the Israeli received a 10-second penalty.
Bearman and Pourchaire’s fight for the lead intensified over the net few laps, with the Frenchman saying at one point that “if I don’t avoid that, we crash.”
Further back, Doohan had made it past Isack Hadjar (Hitech) for eighth at Les Combes.
The first round of stops began at the end of lap 11, including Hadjar, who hit the wall at the pit exit and suffered terminal front wing damage, prompting a virtual safety car.
The hazard was cleared two laps later, with Martins pitting from fourth and Maloney from fifth, exiting in 10th and 11th, though the Alpine junior was handed a five-second penalty for speeding.
Bearman and Pourchaire were next to stop, proving pivotal in the fight for the lead as ART pipped Prema to the quicker stop and handed the Frenchman control of the race.
The safety car was deployed again on lap 16 after Jak Crawford (Hitech) came to a stop on track after contact with VAR driver Juan Manuel Correa, handing Doohan the ideal time to stop for soft tyres and exiting behind Pourchaire and ahead of Bearman.
Racing was about to resume when Joshua Mason, making his debut for PHM this weekend, ran onto the grass and spun at Turn 9, blaming team-mate Nissany for “just stopping.”
The safety car ended the following lap, with Pourchaire backing the pack up before maintaining his lead.
There was a big moment for Martins on lap 22 at Les Combes, coming together with Bearman as he made a move for third, with the Briton receiving a five-second penalty.
Doohan took the lead the next lap on the Kemmel Straight with the help of DRS, moving past Pourchaire on his soft, fresher tyres.
Fittipaldi then made it past team-mate Maloney on the final lap to take fifth, but was promoted to third after Martins and Bearman served their penalties.
Maloney was promoted to fourth, with Martins fifth and Richard Verschoor in sixth for Van Amersfoort Racing.
Bearman was seventh after his penalty, with Kush Maini in eighth for Campos Racing and Trident’s Roman Stanek and Ralph Boschung (Campos) rounding off the top 10.
F2 returns after the summer break at Zandvoort, with the last two rounds at Monza and Abu Dhabi.
F2 Spa - Feature race results:
| Cla | # | Driver | Team | Gap |
|---|---|---|---|---|
| 1 | 14 |
 Jack Doohan |
Invicta Virtuosi Racing | - |
| 2 | 5 |
 Théo Pourchaire |
ART Grand Prix | 1.9 |
| 3 | 4 |
 Enzo Fittipaldi |
Rodin Carlin | 9.1 |
| 4 | 3 | Zane Maloney | Rodin Carlin | 10.1 |
| 5 | 6 |
Victor Martins |
ART Grand Prix | 10.5 |
| 6 | 22 |
 Richard Verschoor |
Van Amersfoort Racing | 10.5 |
| 7 | 8 |
 Oliver Bearman |
PREMA Racing | 12.7 |
| 8 | 24 |
 Kush Maini |
Campos Racing | 13.7 |
| 9 | 20 |
 Roman Staněk |
Trident | 16.5 |
| 10 | 25 |
 Ralph Boschung |
Campos Racing | 17.6 |
| 11 | 12 |
 Arthur Leclerc |
DAMS | 18.9 |
| 12 | 23 |
 Juan Manuel Correa |
Van Amersfoort Racing | 19.7 |
| 13 | 16 |
 Roy Nissany |
PHM Racing by Charouz | 20.6 |
| 14 | 21 |
Clement Novalak |
Trident | 23.8 |
| 15 | 17 |
Joshua Mason |
PHM Racing by Charouz | 25.2 |
| 16 | 15 |
 Amaury Cordeel |
Invicta Virtuosi Racing | 27.9 |
| 9 |
 Jak Crawford |
Hitech Pulse-Eight | 10 laps | |
| 2 |
Jehan Daruvala |
MP Motorsport | 11 laps | |
| 10 |
Isack Hadjar |
Hitech Pulse-Eight | 14 laps | |
| 1 |
 Dennis Hauger |
MP Motorsport | 20 laps | |
| 11 |
 Ayumu Iwasa |
DAMS | 24 laps | |
| 7 |
 Frederik Vesti |
PREMA Racing |
