The Briton, who wrapped up the championship in Texas last month, lapped 0.123 of a second quicker than German team mate Nico Rosberg.
His best lap of one minute 12.070 was set on soft tyres in the final minutes.
Earlier, with some 20 minutes gone, he had crawled to a halt on the track and told the team over the radio that he had lost gears.
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An electronic problem was diagnosed, fixed in the garage and Hamilton returned to set a best time before he then spun off at turn 11.
"I don't know what happened there, but the rear just gave up real quick," he said.
Mercedes technical head Paddy Lowe confirmed there had been an electronics problem which affected the gearshift.
"I think that should be fine for the race," he told Sky Sports F1.
Ferrari's Sebastian Vettel and Kimi Raikkonen were third and fourth fastest, with the German 0.690 off Hamilton's pace but still likely to pose a threat in the race.
Finland's Valtteri Bottas, who has a three place grid penalty, was fifth for Williams with Mercedes-powered cars filling seven of the top 10 places ahead of qualifying.
"It's probably closer than it looks from that timesheet to Ferrari," said Lowe.
Rosberg, last year's winner at Interlagos, is chasing his fifth successive pole position while Hamilton can claim his career 50th.
(Reporting by Alan Baldwin, editing by Pritha Sarkar)
