It is the Alpine Academy member's first win with ART Grand Prix, which he joined from MP Motorsport this season, and marked a change in his fortunes after a forced retirement in the sprint race.
Leclerc made an astonishing charge through the field to finish second for Prema Racing, having started in P13.
Franco Colapinto crossed the line in third place for series newcomer Van Amersfoort Racing, but was demoted to P5 after being hit with a five-second penalty for exceeding track limits, handing the final podium place to ART’s Gregoire Saucy.
Saucy’s teammate Juan Manuel Correa finished in fourth, having held off various challenges throughout the chaotic race, which saw four retirements, one safety car and a VSC.
Colapinto had a great start ahead of Roman Stanek (Trident), with the pair holding the top two spots out of Turn 1.
But seconds later the safety car was deployed after rookies Zane Maloney, driving for Trident, and Francesco Pizzi (Charouz Racing System) both spun to a stop on track, ending their races.
Caio Collet suffered terminal damage in his MP Motorsport car trying to avoid the Barbadian rookie, destroying his front suspension as he came back on track from swerving the spin.
The safety car ended on lap five, before disaster struck for the second consecutive race for Stanek, with contact from MP Motorsport driver Alexander Smolyar’s front wing giving him a puncture, forcing him to pit.
Nazim Azman then also stopped on track in his Hitech Grand Prix-run car, prompting a virtual safety car and making him the fifth driver to retire in as many laps.
Leclerc had made it up to P7 by the seventh lap before taking P6 from Isack Hadjar (Hitech) up the inside of Turn 4.
Correa and Smolyar endured a fierce battle for third on lap eight, with the American driver emerging in front after the middle sector.
By lap 11, Leclerc had snatched P3 from Correa into Turn 1, before continuing his charge past Colapinto at Turn 2 on lap 18.
The fighting behind them had allowed Colapinto and Martins to build up a healthy gap to the pack by the halfway mark before Martins eventually took the lead on lap 15, despite his rival’s best attempts to defend.
Colapinto’s woes continued as he struggled with his tyres before the five-second penalty pushed him out of the podium places.
Leclerc’s teammates Ollie Bearman and Jak Crawford ended the race in P6 and P7 respectively, having started in P10 and P20, marking a strong start to the season for Prema Racing.
Hadjar had looked like a top five challenger early on in the race, but suffered a puncture after contact with Smolyar in an incident similar to that which pushed Stanek to the back of the pack. He went on to finish in P25.
Several drivers were penalised for exceeding track limits alongside Colapinto, with Pepe Marti also handed a five-second penalty while Bearman received a warning.
Enzo Trulli was given a 10-second penalty for causing Azman’s race-ending collision.
F3 returns in Imola from 22-24 April.
