Bottas set an Interlagos track record of 1 minute 8.322 seconds.
Hamilton had been due to line up 20th on the grid on Sunday, requiring approval from the stewards to race after technically failing to qualify for the race.
"In a few occasions, not as many as I would have wanted, I managed to be ahead of him", Bottas told Sky Sports News. "First of all I'm happy everyone is in one piece and nothing physical happened to anyone but it was a pretty bad situation to be in, and I'm happy everybody is still here".
"I just need to take whatever bubble of negativity comes from that experience and move forwards and try and grow from it".
The four-time world champion, who has a 15-point advantage over Bottas in the battle to finish as runner-up to Hamilton, said: "I'd love to be ahead".
The Brazilian Grand Prix is the penultimate race of the season and kicks off at 4pm GMT on Sunday.
"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". 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. It was a nice lap, but it was close with Sebastian (Vettel).
Retirement-bound local hero Felipe Massa of Williams was 10th.
"I think I chickened out a bit on the brakes on the last lap going into Turn One", he said.