The world champion set a quickest lap-time of 1:12.070 with yellow wall soft compound tyre to edge out Mercedes team-mate Nico Rosberg, who was 0.123s slower.
Lewis session was not a perfect, he came to a stop at turn ten after 20 minutes, he radioed in to say he had “lost gears”, this was prompted a double yellow. But, he was able to get his Mercedes back going again without requires a red flag.
Just after first half of the session, Hamilton made a mistake and its results a spin out to run-off area. The Brit looked to be struggling but then set a 1:12.070 to quickest of the session.
Sebastian Vettel made third fastest was 0.690secs behind pace-setter Hamilton and ahead of team-mate Kimi Raikkonen.
Valtteri Bottas took fifth ahead of Nico Hulkenberg’s Force India and Romain Grosjean’s Lotus.
Sergio Perez set eighth fastest ahead Pastor Maldonado, Toro Rosso’s Max Verstappen finished 10th ahead of team-mate Carlos Sainz in 15th.
Jenson Button was 18th in the McLaren, he complained of a difficult balance and front brake locking as he lagged four places and 0.595secs adrift of team-mate Fernando Alonso.
Hamilton, already secured of his third world title, is seeking a first win in Brazil at his ninth attempt.
Rosberg, who won in Brazil last year and is now coming off a victory in Mexico two weeks ago, is seeking to hold off Vettel for second place overall.
Rosberg is 21 points ahead of the fellow-German with two races left and will clinch the runner-up spot if he wins Sunday.