The 26-year-old Finn, who joined the team as replacement for retired 2016 world champion Nico Rosberg, made the most of a less competitive final lap by the Briton to claim the prime starting position for Sunday's race.
"Obviously, I am really happy," said Bottas. "It took a few races, but hopefully it's the first of many."
Bottas clocked a best lap of one minute and 28.769 seconds in the final seconds and it was, as Hamilton admitted, too good for him to beat. Hamilton had clocked 1:28.792.
Hamilton, who was seeking his seventh successive pole position and third in a row this season, gave his team-mate a generous hug after the session.
Three-time champion Hamilton who shares the championship lead with Sebastian Vettel, and who had been quickest until the final runs, was unable to find the extra speed he needed on his second run in Q3 to retain pole position.
- Alonso takes it easy -
========================
Australian Daniel Ricciardo was fourth for Red Bull ahead of Kimi Raikkonen in the second Ferrari, Max Verstappen in the second Red Bull and Nico Hulkenberg who qualified seventh for Renault.
Felipe Massa was eighth for Williams ahead of Romain Grosjean of Haas and Jolyon Palmer in the second Renault.
The conditions at the start of qualifying were cooler, and calmer, than they had been earlier in the day. The air temperature was down to 29 degrees Celsius and the track 31, down by six and eight degrees respectively compared to the earlier free practice session.
In Q2, Indy 500-bound two-time champion Fernando Alonso took it easy.
After another Honda power-unit failure, he decided not to bother at all and was unzipping his overalls without seeking a place in the top ten shootout.
The McLaren man qualified 15th behind the four who were eliminated -- Daniil Kvyat of Toro Rosso, Canadian rookie Lance Stroll of Williams, Pascal Wehrlein of Sauber and Esteban Ocon of Force India.
Team-mate Palmer grabbed 10th to secure Renault's first double showing in Q1 since the 2011 Japanese Grand Prix.
As the shootout began, the Red Bulls led the two Mercedes out for their final flurry, Ricciardo starting with a 1:30.007. That time was overhauled by Bottas in 1:28.844 -- the first man inside Hamilton's 2016 pole lap -- and then by the Briton in 1:28.792.
Vettel was four-tenths down for Ferrari after the first runs, which saw Raikkonen adrift by a similar gap before the final drama unfolded.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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