Monaco victor Jazeman Jaafar claimed second place for Fortec, finishing 6.8 seconds ahead of Red Bull junior driver Dean Stoneman, and retains the lead in the championship by five points over Vaxiviere.
Away from the lights, Canadian rookie Nicholas Latifi jumped poleman Vaxiviere from the outside of the front row to lead a chaotic opening lap.
Behind, Vaxiviere's Lotus team-mate Meindert van Buuren was tapped into a spin after being hit by Sean Gelael on the entry to La Source and received a puncture.
The run into Les Combes for the first time proved frantic. At a congested apex, Manor Formula 1 driver Roberto Merhi was punted into a pirouette by a Tech 1 car, sending several competitors across the run-off in avoidance.
Pons racer Merhi had been backing out of a passing attempt on Oliver Rowland, who had earlier lost a position to fellow Briton Stoneman in a tight move at Eau Rouge that had cost him momentum.
The final incident on the opening tour occurred four corners later, and required the presence of the safety car. The unfortunate Pietro Fantin found the barriers on the exit of Bruxelles to sustain his second sizeable crash of the weekend.
Vaxiviere made his bid for the lead on lap six, first challenging Latifi on the outside of Spa's traditional overtaking spot Les Combes, before making a bold pass around the outside into Pouhon.
Once in clean air, Vaxiviere streaked away to achieve a five-second winning margin.
The Gravity-managed driver was aided in making his break by a fierce battle for second disputed between Latifi, Jaafar and Stoneman.
Petronas-backed Jaafar achieved a superior exit to Latifi at La Source on lap seven to fleetingly steal the position.
As an opportunistic Stoneman also sought to make a move on the Arden driver, the trio arrived at Les Combes in close proximity.
Minor wheel-to-wheel contact was made between Jaafar and a stubborn Latifi, and the Formula 3 graduate took to the escape road before rejoining back in second position.
Rather than relinquish his position, Latifi held on until Blanchimont where he committed a small error and allowed Jaafar to recover the place, while Stoneman passed the Canadian for good into La Source at the start of the next tour.
Stoneman appeared secure in third until running wide over the kerbs at the Bus Stop chicane six laps from home, but survived the late drama to achieve his second successive podium.
Behind Latifi, Oliver Rowland finished fifth, edging out Carlin's GP2 veteran Tom Dillmann by 1.1s.
It was a day to forget for the AVF team. An extra formation lap was required when Alfonso Celis Jr stalled from an unlucky 13th on grid.
The Mexican's team-mate Beitske Visser did not participate in the race after her investors asked her to withdraw.
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