Hamilton's Ferrari title rival Sebastian Vettel, 40 points behind the Briton with six races remaining in the battle of four-times world champions, will start third at the Black Sea circuit on Sunday.
"It feels good," said Bottas. "Coming to this weekend I knew that normally it's been a pretty good track for me and again I managed to get some good laps in. The car just felt really strong."
The pole, in a track record of one minute 31.387 seconds, was only the second this season for Bottas, who is 110 points behind Hamilton.
It also came at the track where last year he celebrated his first win.
"He's driven brilliantly this weekend and he just did a better job," said Hamilton, who had been fastest in the first two parts of the session and looked set for a career 80th pole until he went wide at turn seven.
"My last two laps of Q3 weren’t great -- you can’t always have it -- but we’re still in contention for tomorrow," added the Briton, who will be chasing his eighth win of the campaign.
"It's a long way down to turn one so we'll still have a fight at least tomorrow."
Team boss Toto Wolff said Bottas "was so pumped the adrenaline was coming out of his ears" but left open a question about whether Mercedes would enforce team orders in Hamilton's favour come race day.
TABLES TURNED
Vettel, who had led an all-Ferrari front row in Russia last year with Bottas third, hoped Sunday could see the tables turned.
"I just spoke to Valtteri and reminded him what happened last year so maybe we can turn that around this time," the German told reporters.
"It was important to get as close to them but it is true they have been very quick. It is a long race and the tyres will be important. We should've been a lot closer," he added.
"The car felt alright so that makes me happy. If there is a gap we will go for it."
The second phase of qualifying had a strange feel to it, with five cars -- the two Red Bulls, Renaults and Toro Rosso's Pierre Gasly -- doing no laps as a consequence of grid penalties.
Renault had no need to do anything, since the other three cars were all going to start at the back of the grid, and failure to qualify in the top 10 gave them the benefit of tyre choice.
Denmark's Kevin Magnussen will line up in fifth place for Haas, behind Ferrari's Kimi Raikkonen, with Frenchman Esteban Ocon -- highly rated but looking increasingly likely to be sitting out next season -- sixth for Force India.
"It's strange being best of the rest," commented Magnussen. "You don't want to get involved with the guys in front as that can mess up your own race. Hopefully I will have a clean track."
Sauber's Ferrari-bound rookie Charles Leclerc qualified seventh.
McLaren and Williams filled the last four slots but that will change once Red Bull's Daniel Ricciardo and Max Verstappen, along with Toro Rosso's Gasly and Brendon Hartley, take their penalties.
That should at least give the crowd some overtaking to look forward to and Verstappen something to make his 21st birthday more exciting.
(Reporting by Alan Baldwin, editing by Clare Fallon)
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