The Australian started 11th but rose through the field in the early laps before a well-timed Safety Car saw him emerge second to Theo Pourchaire.
With a tyre advantage in the final laps, Doohan stormed by the Frenchman to take victory, and fastest lap, as he climbed to fourth in the F2 standings.
Before the race start, Frederik Vesti and Victor Martins both had moments on their way from the pits to the grid.
The former slid into the wall at Les Combes, and was a scratching from the front row as a result, while Martins was able to recover and take his place in third.
It left Oliver Bearman alone on the front row, the Prema driver taking an easy lead into La Source.
Behind him, Martins had a shocker and slipped to fifth behind Theo Pourchaire, Zane Maloney, and Enzo Fittipaldi.
Hauger had been caught out at La Source when a fast starting Ralph Boschung bogged down on exit, forcing him onto the kerb and deeper into the pack.
The MP Motorsport driver did get going once more, and rejoined the fray a lap behind after bump-starting the car with the help of marshals – for which he would be disqualified.
For his part, Iwasa made it around to the pits where his car was retired.
Racing resumed at the start of Lap 4, Martins making short work for Maloney to take fourth.
There was a hairy moment for Arthur Leclerc as he spun at Raidillon, though didn't hit anything and was able to limp back to the pits with nothing more than a right-rear puncture.
Simultaneous mistakes from Bearman and Pourchaire as they battled for the lead saw the pair skip through the apex of Les Combes.
They'd extended a comfortable advantage over Fittipaldi behind, with Pourchaire in DRS range of Bearman.
In truth, Pourchaire wasn't close enough to make a move stick, but he was able to pressure his rival into a mistake.
It was a tactic he employed next time around without success, though the pair came close to contact which prompted an angry radio call from the Sauber Academy member.
On Lap 8, Jack Doohan moved up to eighth, passing Isack Hadjar around the outside at the Fagnes chicane.
Of the front runners, Jehan Daruvala was the first to pit Lap 11, heading into the lane from seventh place.
Soon after, the Virtual Safety Car was called for when Hadjar clouted the barrier exiting the lane, knocking the front wing off his car.
It was a brief interruption and racing soon resumed, Bearman still leading from Pourchaire with Doohan up to seventh.
Martins and Maloney were in the lane on Lap 13, prompting Prema to call in Bearman from the race lead.
The battle at the front had become a three-way contest with Fittipaldi having joined Pourchaire, with Richard Verschoor in fourth more than six seconds adrift.
Pourchaire also pitted, his stop quicker than Bearman as he cleared the pole-sitter as they exited the lane.
He only narrowly avoided losing out to Fittipaldi too, the Brazilian emerging in the lead but was passed on the run to Eau Rouge as he exited the pits by boith Pourchaire and Bearman.
With the pit cycle yet to be completed, Doohan held the lead.
He boxed after 15 laps, a timely choice as the Safety Car was deployed when Jak Crawford stopped at Les Combes following contact with Juan Manuel Correa.
The Australian emerged second to Pourchaire in the queue, a strong gain with a set of soft compound tyres fitted, versus the mediums for those around him.
Behind the Safety Car, the order ran Pourchaire from Doohan, then Bearman, Martins, Maloney, and Fittipaldi.
Racing was set to resume on Lap 20, but that was waved off when Josh Mason had a bizarre moment – appearing to simply steer off the road on approach to Pouhon and spin on the wet grass.
It delayed proceedings by a lap as the hapless Brit, whose debut F2 weekend has done his career prospects no favours, recovered to the back of the queue once again.
At the restart, Pourchaire held the field, accelerating only 100 metres from the braking zone for the final chicane.
Pourchaire Pour and Doohan quickly pulled clear, the Australian locked on with a tyre advantage in the final five laps.
Behind them, Martins saved a potentitally mammoth crash at Les Combes as he passed Bearman for third.
The Frenchman had used DRS to pass the pole man, who then attempted to tuck into his slipstream too early, tagging his rear wheel.
It saw Martins slew sideways, and he did well to hold the car – though he took to the escape road, he quickly returned without losing a place.
With three laps remaining, Doohan surged into the lead on the Kemmel Straight, using DRS to breeze by Pourchaire.
Doohan went on to claim the point for fastest lap, catapulting him back into championship contention.
Pourchaire was second while Fittipaldi claimed third after Martins picked up a time penalty for speeding in the pit lane.
Bearman too picked up a penalty, his for contact with Martins, which elevated Fittipaldi to the podium after he passed Zane Maloney on the final lap.