Sunday's race is the penultimate round of the season.
Brendon Hartley made his F1 debut in Texas and is now set to also compete in Mexico, Brazil and Abu Dhabi.
The 32-year-old, who secured his fourth drivers' world championship at the Mexican Grand Prix at the end of October, lost control of his Mercedes and slewed off into the barriers at Turn Six of the Interlagos circuit.
"It was a shame that Lewis is out, a shame for us, but I stood up for the team and it is good to start from pole position here". Sebastian Vettel of Ferrari was second, Kimi Raikkonen of Ferrari third, and Max Verstappen of Red Bull fourth. Ricciardo faces a ten-place grid penalty from wherever he qualifies after a change to his car's MGU-H ahead of Friday practice. The laps were getting better and better, but it was all the time very close, so I'm pleased that in the end I could get it all together in Q3, get a good lap and put it on pole.
"Lewis was out at the beginning which is a shame for us, but I stood up for the team".More news: Sheep can recognise human faces
Hartley finished nearly two seconds slower than Bottas in 17th place.
It was Ferrari duo Raikkonen and Vettel who showed the early pace as they raced to the top of the timesheets ahead of Hamilton and Bottas.
Hamilton, who won his fourth Formula One championship two week ago in Mexico, walked away from the vehicle without appearing injured and will start at the back of the grid on Sunday.
"It is what it is, of course it's unfortunate, I tend to just look at it as... challenges are what makes life interesting, and overcoming them makes life meaningful", Hamilton said.
"I'm OK. It happened really quickly", Hamilton said. "I'm looking forward to tomorrow". "Years ago I came from quite far behind and had a great race".