The Briton lapped the resurfaced Sepang circuit in one minute, 34.434 seconds on a sweltering afternoon with track temperatures approaching 50 degrees Celsius.
The Mercedes driver's benchmark was 0.445 seconds quicker than the best managed by Max Verstappen, whose late flying lap vaulted him up to second for Red Bull, splitting Hamilton and his championship-leading team mate Nico Rosberg.
Hamilton's pace was nearly a full five seconds clear of the fastest time recorded at the track in the dry last year.
Ferrari's Kimi Raikkonen set the fourth-fastest time ahead of team mate Sebastian Vettel, last year’s winner, who knocked out a trackside bollard in an otherwise harmless spin at the final corner.
Australian Daniel Ricciardo was sixth for Red Bull, about a second adrift of Hamilton and ahead of Force India's Nico Hulkenberg.
Valtteri Bottas and Felipe Massa were eighth and tenth, respectively, for Williams, sandwiching the Toro Rosso of Carlos Sainz.
Fernando Alonso, set to start at the back of the grid on Sunday, propped up the time sheet.
The Spaniard, who only plans to put in one lap good enough to assure him a place on the 22-car grid later on in qualifying, appeared to be focussed on honing his McLaren's long run pace.
He will be carrying a further 15-place engine-related grid penalty after his team opted to fit his car with a fresh turbo-charger and MGU-H hybrid component on Saturday.
The twice world champion was already due to drop 30 places for trialling Honda's updated engine in Friday practice.
Mercedes head into Sunday's race firmly on course to wrap up their third straight constructors' title but the battle between their two drivers remains as tight as ever.
Rosberg holds an eight point advantage over Hamilton in the overall standings after winning the last three races.
(Editing by Nick Mulvenney)
