Bottas took advantage of Hamilton’s demise to beat Sebastian Vettel to pole position.
The Finn edged out Vettel by just four hundredths of a second to land his first pole since July’s Austrian Grand Prix.
“It is a good feeling,” said Bottas, who is just 15 points behind Vettel in the race for second place in this year’s championship.
“It was a nice lap and I was so close with Sebastian through qualifying so it was great to get a good lap in.
“Lewis was out at the beginning which is a shame for us, but I stood up for the team.”
Kimi Raikkonen will line up in third on the grid ahead of Red Bull’s Max Verstappen.
Daniel Ricciardo qualified fifth, but he will be demoted to the back of the grid following a series of engine penalties.
Ricciardo’s penalty promotes Force India’s Sergio Perez to fifth, with McLaren driver Fernando Alonso to line up in sixth.
Brendon Hartley and Pierre Gasley also received engine penalties while Lance Stroll was penalised for a gearbox change.
Click through the gallery above to see the starting grid for tomorrow’s Brazilian Grand Prix!