The German lapped a damp and overcast Interlagos circuit with a best time of one minute 11.740 seconds, with reigning triple world champion Hamilton a mere 0.093 slower.
Ferrari's Sebastian Vettel and Kimi Raikkonen were third and fourth, with Red Bull pairing Max Verstappen and Daniel Ricciardo fifth and sixth.
Rosberg will take his first title on Sunday if he wins the penultimate race of the season, but the battle will go down to the finale in Abu Dhabi if he otherwise fails to score seven points more than his team mate.
The Mercedes drivers are the only championship contenders, divided by 19 points. Rosberg has nine wins to Hamilton's eight.
The weather could also play a big part in Sunday's outcome, with forecasts predicting an increasing likelihood of rain in the afternoon.
(Editing by Ed Osmond)
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