Valtteri Bottas grabbed his first ever pole position, beating Lewis Hamilton to top spot
Sebastian Vettel set the fastest lap-times in both of Friday's practice sessions but it was Red Bull's Max Verstappen who excelled in the final dash before qualifying, overcoming the windy conditions to set the quickest lap.
However, Mercedes turned it on at exactly the right time in signature style but it was Bottas and not Lewis Hamilton who set the fastest time to record his first ever pole.
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Bahrain Grand Prix qualifying three results
1st Valtteri Bottas, 2nd Lewis Hamilton, 3rd Sebastian Vettel, 4th Daniel Ricciardo, 5th Kimi Raikkonen, 6th Max Verstappen, 7th Nico Hulkenberg, 8th Felipe Massa, 9th Romain Grosjean, 10th Jolyon Palmer.
Hamilton put it on provisional pole in the early stages of the final session but Bottas put the pressure on with a quicker lap in the closing minutes.
The Brit was expected to have the pace to get past him but time on his team-mate in the middle sector which proved to be crucial.
Vettel was the best of the rest in third but was more than four tenths of a second behind his championship rival while Daniel Ricciardo started to get his season back on track, beating Kimi Raikkonen and his Red Bull team-mate Max Verstappen into fourth spot.
Bahrain Grand Prix qualifying two results
Eliminated: Fernando Alonso (McLaren), Lance Stroll (Williams), Esteban Ocon (Force India), Daniil Kvyat (Toro Rosso), Pascal Wehrlein (Sauber).
The story of Q2 was the pace of Jolyon Palmer, who got into Q3 for the first time in his F1 career.
His Renault team-mate Nico Hulkenberg also produced a fine lap, the fifth fastest of the session, to put both cars into the final session.
Lance Stroll had some technical issues and was sent out in the Williams with just one chance to set a qualifying time.
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And the young Canadian made a small mistake in the final corner which saw him drop out of the top 10.
Fernando Alonso did not set a time in the second session of qualifying after arriving back in the pits with the engine off during Q1 as the McLaren-Honda struggles continued.
Bahrain Grand Prix Q2 results
Bahrain Grand Prix qualifying one results
Eliminated: Stoffel Vandoorne (McLaren), Carlos Sainz (Toro Rosso), Marcus Ericsson (Sauber), Sergio Perez (Force India), Kevin Magnussen (Haas).
The main surprise was the impressive Carlos Sainz, who drove brilliantly in China, but having gone fastest in sector one his car stopped in the final part of the lap. The Spaniard said he "lost power" and was eliminated in 16th place.
Esteban Ocon had a problem with his DRS rear wing and was forced to return to the pits where his Force India crew were able to fix it and he snuck through by four tenths of a second.
Romain Grosjean crashed in Saturday practice and had been complaining of problems with oversteer and then braking but he was able to produce a lap worth of a place in Q2.
However, his team-mate Kevin Magnussen was not able to replicate his pace.