The Trident polesitter repeated his stellar drive at Spa to take back-to-back wins, having also taken a podium at the Hungaroring.
Despite Martins taking the lead off the line, Maloney recaptured the front spot at the halfway mark before enduring two safety car restarts to take victory.
Martins, finishing second for ART, now leads the standings by five points from Isack Hadjar heading into the final round at Monza.
Franco Colapinto rounded off the podium for Van Amersfoort Racing at its home race, his fourth visit to the rostrum of the year.
Martins immediately took the lead into Turn 1, with Maloney wide across the grass at the exit but holding second into Turn 2.
A poor start from Ollie Bearman further back saw him drop from 14th to 18th, putting him into a fight with Prema teammate Arthur Leclerc, who started 20th.
The safety car was first deployed on lap three, with Brad Benavides (Carlin) rear-ending Jenzer’s William Alatalo into Turn 2 after locking up, sending both into the gravel and ending their races.
Racing resumed five laps later, with Martins leading the field away as Jak Crawford locked up, falling from third down to ninth and allowing Colapinto into the podium places.
MP Motorsport driver Caio Collet and Sebastian Montoya, taking part in his debut F3 weekend for Campos, then passed Jonny Edgar (Trident) into seventh and eighth respectively.
Up front, Maloney retook the lead out of Turn 1 on lap 12 in a replica of the move Martins used to lead initially.
Crawford was shown the grass again the following lap under pressure from Carlin’s Zak O’Sullivan, but managed to hold onto ninth, before clawing his way up to seventh by lap 14 with DRS.
Racing was once again neutralised on lap 19, with David Vidales beaching his Campos Racing car in the gravel at Turn 2.
With just five laps remaining, the green flag was waved again, with Colapinto closing in on Martins as Maloney held the lead.
Further back, Bearman had made it up to 11th, passing two drivers in as many corners before an aggressive move up the inside of O’Sullivan to take 10th.
The safety car was again deployed just three laps from the end of the race after Rafael Villagomez (VAR) came off at Turn 1 and became lodged, while Gregoire Saucy (ART) retired after suffering damage to his front-right steering arm.
Maloney led the pack as the safety car ended with two laps remaining, and managed to hold on to cross the line despite Martins looking close on the restart.
Roman Stanek took fourth for Trident, with title contender Hadjar in fifth for Hitech. Collet lost sixth to Crawford on the final lap after locking up at Turn 1, with Montoya in eighth.
Edgar and Bearman rounded off the top 10, though the Prema driver faces an investigation for his move on O’Sullivan.
