Hamilton, who wrapped up his fourth Formula 1 drivers' championship title in Mexico a fortnight ago, is determined to end the season on a high, with victories at Interlagos on Sunday and the season's finale in Abu Dhabi on November 26.
But Bottas is also keen to prove he will be able to challenge Hamilton for the world title at the Silver Arrows in 2018 and the Finn pipped him by the smallest of margins to secure a confidence boost ahead of Saturday afternoon's qualifying session.
The top four were separated by just 0.058secs as the Ferrari pair of Kimi Raikkonen and Sebastian Vettel followed the Mercedes cars.
Red Bull's Daniel Ricciardo was fifth, 0.9secs off the pace, while his team-mate Max Verstappen, who has won two of the last four races, took a spin which left him down in ninth.
It was a good session for McLaren's Fernando Alonso as the two-time world champion was sixth fastest - 0.1secs ahead of the Force India duo of Sergio Perez and Esteban Ocon.