Hamilton finished 0.148 seconds clear of Leclerc, while McLaren's Lando Norris was third, 0.499secs off the pace. Red Bull's Max Verstappen ended the day fourth fastest.
Fernando Alonso finished 19th in Aston Martin's heavily revised car after what team principal Adrian Newey described as a "promising" debut for the package, which features a new chassis and aerodynamic concept while retaining the existing engine, gearbox and front suspension.
The Spaniard was 2.990secs slower than Hamilton, although a lap nearly four-tenths quicker was deleted for exceeding track limits at the final corner.
While Aston Martin remain some way off the front-runners, the updated car appears to represent a notable step forward compared with the team's form for much of the season.
Ferrari looked competitive throughout the sessions, as expected on a circuit that suits the SF-25's strong cornering characteristics.
Mercedes, however, appeared to have work to do. George Russell finished fifth, 0.933secs behind Hamilton, while championship leader Kimi Antonelli could manage only 13th after a disrupted afternoon.
Antonelli failed to complete a representative qualifying simulation. His first attempt was abandoned after Franco Colapinto crashed his Alpine at the final corner, while an error at the chicane ended his second flying lap.
The Italian also spent much of the session complaining about rear brake locking, although he had matched Norris through the opening sector on both interrupted laps before they were cut short.
Red Bull's Isack Hadjar was sixth fastest, followed by Racing Bulls team-mate Liam Lawson in seventh. McLaren's Oscar Piastri finished eighth, with Audi's Nico Hülkenberg and Racing Bulls rookie Arvid Lindblad rounding out the top 10.
