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 had immediately taken the lead into Turn 1, with Maloney wide across the grass at the exit but holding second into Turn 2.
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.
But, up front, Maloney retook the lead out of Turn 1 on lap 12 in a replica of the move Martins used to lead initially, and set about attempting to build a lead as the French driver struggled more with his tyres in the second half of the race.
Racing was once again neutralised on lap 19 as David Vidales parking his Campos-run machinery at Turn 2 with an apparent mechanical issue, and the full safety car was required to get his car cleared safely.
With just five laps remaining, the green flag was waved again, with Franco Colapinto closing in on Martins as Maloney held the lead.
As Maloney had just streaked clear once more, the safety car was again deployed just three laps from the end of the race after Rafael Villagomez (VAR) came off at Turn 1 while duelling with Juan Manuel Correa and became lodged in the gravel, 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 closer on the restart.
Franco Colapinto rounded off the podium for Van Amersfoort Racing at its home race, his fourth visit to the rostrum of the year.
Roman Stanek took fourth for Trident, with title contender Isack Hadjar in fifth for Hitech. Caio Collet lost sixth to Crawford on the final lap after locking up at Turn 1, with Sebastian Montoya - in his first F3 round - finishing in eighth.
Collet had challenged Hadjar for fifth earlier in the race which could have swung the title lead further in his Alpine Academy stablemate Martins' favour, but was unable to lodge an assault.
Jonny Edgar and Oliver Bearman rounded off the top 10, though the Prema driver faces an investigation for his move on Zak O’Sullivan.
A poor start from Bearman meant that he'd dropped from 14th to 18th, putting him into a fight with Prema team-mate Arthur Leclerc, who started 20th.
But in a stirring display, Bearman had made it up to 11th - passing Alexander Smolyar and Gregoire Saucy at Turns 7 and 8 respectively on the same lap before an aggressive move up the inside of O’Sullivan to take 10th.
Martins, finishing second for ART, now leads the standings by five points from Isack Hadjar heading into the final round at Monza.
FIA F3 Zandvoort feature race results - 26 laps
