The Monegasque, who heads into the weekend on a high after successive wins in Belgium and at Ferrari’s home race in Italy, pumped in a lap of one minute 38.192 seconds as the sun set over the Marina Bay street track.
That was good enough to lift him 0.207 seconds clear of Formula One world championship leader Lewis Hamilton, who was second for Mercedes.
The Briton, who leads team mate Valtteri Bottas by 63 points in the overall standings and was fastest on Friday, spun while leaving the pits.
Singapore Grand Prix
Vettel takes first win in over a year ahead of furious Leclerc
He was then forced to abandoned his initial attempt at a fast lap when he came up behind slower cars.
The five-times world champion still split his Ferrari rivals with his time good enough to beat Sebastian Vettel who was third, 0.619 seconds off Leclerc’s pace.
Leclerc had ended Friday practice with only the sixth fastest time after also suffering gearbox problems that left him 19th during the opening 90 minutes of running.
Despite their back-to-back success on the flat-out straights of the Spa and Monza circuits, Ferrari were expected to struggle in Singapore which has more corners than any other venue on the calendar.
Leclerc’s time in final practice marked him out as a likely contender in qualifying for a fifth career pole and third in a row.
Valtteri Bottas, who crashed during Friday’s opening practice session, was fourth fastest and British-born Thai rookie Alexander Albon fifth for Red Bull with team mate Max Verstappen sixth.
Red Bull have finished second for the last five years on a track which winds its way through the heart of the glittering city-state and has tended to suit the team’s typically nimble car.
Carlos Sainz set the seventh fastest time ahead of McLaren team mate Lando Norris.
The session was briefly halted after Sergio Perez brushed the barriers. The impact punctured his tyre and broke his wheel rim, scattering debris across the track.
Daniil Kvyat failed to set a time, pulling into the pits with his Honda-powered Toro Rosso trailing smoke.
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