Hamilton lost out by just six-thousandths of a second, while Bottas stormed to his fourth pole position of the season, following his three in a row from China, Azerbaijan and Spain earlier this year.
Both Mercedes drivers set their fastest times on the first time around, as the grip wasn't there for the final laps. Hamilton made a mistake at the end of sector one on his quickest time, which he feels cost him the shot at pole.
"Firstly congratulations to Valtteri, he did a solid job all through qualifying," Hamilton said. "Ultimately it wasn't good enough. We worked really hard throughout the session and it just got away from is.
"We sacrificed a lap in Q2 which would have helped us get an understanding of how the car was. But we didn't end up doing that. At the end, I had that mistake on the first lap and the second lap just wasn't that great.
"But fair play to Valtteri, who did the job. But it's a long race tomorrow."
Hamilton also offered his gratitude to the fans around the circuit, who made noise for him as he was being interviewed post session.
"It's the best Grand Prix of the year. It's incredible, the energy that these people bring. These tracks have great layouts, designs, good area and space but without the people, there's no energy."