The feature race at Monza was stopped on lap 16 after Kush Maini (MP Motorsport) spun at the exit of Lesmo 2, collecting Brad Benavides on their way into the barrier.
This had prompted the cars to return to the pitlane, but Martins was then handed a five-second penalty, having previously been waved the black and white flag for exceeding track limits on lap seven.
The penalty demoted Martins from third to fifth, but when fourth-placed Jenzer driver William Alatalo was also awarded a five-second penalty, it promoted Martins back up to the fourth place he needed to secure the title.
Maloney's race victory earned the Barbadian second in the championship, having fended off Martins and Oliver Bearman as the trio contended for the title on track prior to the red flag.
At the start, Maloney had passed Trident team-mate Roman Stanek off the line before taking the lead from polesitter Alexander Smolyar at Turns 1 and 2.
But racing was interrupted almost immediately by a first-lap safety car, deployed after David Vidales (Campos) and Van Amersfoort Racing’s Rafael Villagomez ran into the gravel at the first Lesmo.
Racing resumed on lap five, and Maloney elected to get racing back to full speed early - but with the drivers behind grabbing a tow along the start-finish straight, he was vulnerable to attack from Smolyar. The Russian got ahead into the corner before locking up, delaying Maloney as he ran deep, allowing Martins to pass both and claim the lead into the second chicane.
Starting lap eight, Maloney also passed Smolyar into Turn 1, before reclaiming the lead from Martins on the following tour.
Behind, Bearman was brought into play as Stanek and Arthur Leclerc ahead were forced to take to the Turn 1 exit road, slaloming through the bollards and losing time after Leclerc was pitched across Smolyar's bows.
Bearman then passed Smolyar for third at Ascari, the MP Motorsport driver eventually retiring from suspension damage sustained in a brush with Stanek.
Bearman took second from Martins down to Turn 1 on lap 12, and Prema driver soon closed on Maloney. He was within 0.5s of the Trident driver by the following lap, almost clinching the lead at Turn 1 as Maloney locked up.
But the red flag for the collision between Maini and Benavides brought the race to a shuddering halt and, due to scheduling, the race was not restarted.
After Martins' penalty, Jak Crawford was classified behind Maloney and Bearman in third having avoided the earlier skirmish between Leclerc and Stanek.
This cemented the teams' title for Prema, which deposes 2021 winner Trident from the crown.
Behind Martins, Leclerc thus finished fifth, with Stanek and Alatalo classified in sixth and seventh respectively after the Finn's penalty rescued Martins' title.
Jonny Edgar finished eighth for Trident, with Hitech driver Isack Hadjar, who had been a strong title contender until he crashed out of Friday’s qualifying session, in ninth and Reece Ushijima rounding off the top 10 for VAR.
