The Brit left it late to secure top billing as on his final lap of qualifying he posted a time of 1:40.593 to edge out Bottas by just four tenths of a second.
Red Bull had hoped to mount a challenge in qualifying, having topped both Friday sessions with Max Verstappen, but could only manage fifth with Verstappen and 10th with Daniel Ricciardo after he made contact with the wall in the final part of qualifying.
Force India followed up on its promising practice pace with sixth and seventh on the grid ahead of the two Williams of Lance Stroll and Felipe Massa. "Every now and then you call upon it and you don't actually extract it, but it was a ideal lap".
Hamilton made a mistake on his first lap in final qualifying and was anxious he would not be able to make amends when a crash halted the session.
"I am so pumped with that pole, and that is how qualifying should be", Hamilton said. It was a lot of pressure.
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He added: "Bridging between Churchill and Monet, I am certainly a determined optimist". Both sides want transparency to be the default.
"The first lap I had the time but I made a mistake", he added.
Lewis Hamilton: "When I started that lap, I knew where I had to get the tyres to". "We need to get on top of that because it shouldn't happen".
"Coming down to the last corner I was just thinking "please be enough".
"Tomorrow is going to be a long hard race, but we are in the best position to start it".
"The result is Ok but I'm not entirely happy", he said. "As I said other people were doing a better job and therefore their qualified in front of us".
"I'm no fan of excuses, I could have done a bit better but probably P3 was the maximum".
With five minutes to go in Q2, the drivers stuck in the elimination zone were Kevin Magnussen, Nico Hulkenberg, Carlos Sainz, Danill Kvyat and Pascal Wehrlein who had spent the majority of the session in danger of being knocked out.
Fernando Alonso, already hit with a 40-point grid penalty, failed to advance past Q1 for the first time this season, while Jolyon Palmer did not take part in qualifying after a fire in his vehicle during Saturday morning's practice.
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