The Briton put in a best lap of one minute 09.050 seconds, with Red Bull’s championship leader Max Verstappen second and 0.367 slower at an overcast Interlagos with occasional drops of rain and plenty of empty seats in the stands.
Verstappen leads Hamilton, who picked up the penalty for an engine change and complained that the front end of his car was “really poor”, by 19 points with four races remaining including Brazil.
Red Bull’s Mexican Sergio Perez was third on the timesheets with Hamilton’s team mate Valtteri Bottas fourth in the day’s only practice session before qualifying for Saturday’s sprint race.
The 100km sprint offers points for the top three in 3-2-1 sequence and Hamilton’s penalty will only apply to Sunday’s starting grid.
AlphaTauri’s Pierre Gasly was fifth fastest ahead of the Ferraris of Carlos Sainz and Charles Leclerc.
Ferrari reclaimed third place overall from McLaren at the previous race in Mexico and are looking to extend their advantage.
McLaren had Lando Norris 15th and Australian Daniel Ricciardo 19th, but they were running a different programme to the others.