Ferrari had looked quickest all weekend, although as track conditions cooled, it was Mercedes who prevented pole for the prancing horse.
Lewis Hamilton had looked set to take pole after setting a blistering first run, being the first driver to dip into the 1m40s.
However, an unusual tactic by Mercedes saw both drivers do a practice start before their final runs in Q3 – leaving them compromised in traffic.
It left both drivers fighting for track position, but Bottas was able to stay ahead of Hamilton before the start of their final runs and pipped Hamilton to pole.
What went wrong for Ferrari
Despite putting in a strong final lap in Q3, Sebastian Vettel could only take third, three tenths down on Mercedes.
The German survived a few scrapes with the wall during qualifying, but it was his team-mate Charles Leclerc who paid the bigger price for similar mistakes.
Ferrari had opted to try and make it through Q2 on the medium tyres, although Leclerc locked up on his second run and hit the wall in what he branded “stupid” at the castle section of the circuit.
It forced the Monegasque to retire from the session, but due to completing a time that was good enough to get into Q3, he will start the race ninth after penalties.
It will be a disappointing day for Leclerc, who arguably had the pace to take pole position.
Max Verstappen went fourth fastest after opting to do two runs on the same set of tyres in Q3 instead of using a fresh set of tyres for his final run.
Midfield set-up a treat
The midfield threw up unexpected results, with Sergio Perez claiming Racing Point’s best qualifying result of 2019, going fifth fastest.
Daniil Kvyat also impressed by going sixth for Toro Rosso after crashing in practice, with Lando Norris doing a good job for McLaren in seventh.
Despite having to take a 10 place grid penalty for taking a new control electronics this weekend, Antonio Giovinazzi took an impressive eight, with his team-mate Kimi Raikkonen behind in ninth.
Renault struggled throughout the weekend, with Daniel Ricciardo struggling to get out of Q2 and Nico Hulkenberg out in only Q1.
Red Bull’s Pierre Gasly showed impressive pace in Q1 after setting the fastest time, but will start from the pitlane after missing the weighbridge in FP2.
Williams were slowest in qualifying, with Robert Kubica suffering a similar fate to Leclerc after also crashing in the castle section in Q1.