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Vettel pipped team mate Kimi Raikkonen, the duo separated by just 0.143s, in what is the first non-Mercedes pole in Bahrain in six years, with Valtteri Bottas the leading Mercedes in third.
Lewis Hamilton was fourth quickest, but will start tomorrow’s race ninth after a five-place grid penalty for a gearbox change. He could still figure, though, as he’ll be the only driver in the top 10 to start on the soft, rather the supersoft tyre.
Raikkonen and Vettel confirmed the pace Ferrari have demonstrated over one lap so far this weekend by topping the timing charts in Q1, with the duo able to get through using the soft tyre – the middle compound available in Bahrain – and requiring just one flying lap.
Bottas, who was the only other driver to run the soft with everyone else on the supersoft, was third quickest, outpacing his team mate Hamilton by just over a tenth of a second.
Verstappen slotted in ahead of Hamilton in fourth, but left himself with it all to do on Sunday when he crashed on his next run, losing control coming out of Turn 2 and ending up in the barrier nose first.
It meant the Red Bull driver failed to reach Q3 for the first time since the 2017 Chinese Grand Prix.
Race director Charlie Whiting red-flagged the session while the stricken Red Bull was recovered, with Verstappen climbing out of the car and reporting he was unscathed.
On resumption, everyone below sixth-placed Daniel Ricciardo in the other Red Bull headed out for another run, with McLaren’s Fernando Alonso scraping through into Q2 with the 15th quickest time.
Romain Grosjean, who admitted the out lap was a mess and ran slightly wide at the final corner on his last run for Haas, set an identical time to Alonso, forcing him out of qualifying.
The Saubers of Marcus Ericsson and Charles Leclerc, who spun on his final lap and said on team radio that “I am so stupid”, plus the Williams of Sergey Sirotkin and Lance Stroll were also eliminated in the opening phase.
With Hamilton hampered by that five-place grid penalty, he and Mercedes opted to run the softs in Q2, giving him an alternative strategy as he will start the race on that tyre.
Hamilton eased into the final part of qualifying, looking more comfortable on the slower soft tyre to go second. Everyone else was on the supersofts, with Vettel pumping in a brilliant lap to go quickest.
Raikkonen ended up third fastest, with Ricciardo fourth and Bottas fifth with Renault’s Nico Hulkenberg best of the rest in sixth, 0.846s off the pace.
But perhaps the star of the session was Pierre Gasly, who put the Honda-powered Toro Rosso into Q3 for the first time this year in ninth. Team mate Brendon Hartley, who damaged his front wing when he hit a bird early in the session, just missed out in 11th.
Force India’s Sergio Perez was also eliminated, along with Alonso, McLaren team mate Stoffel Vandoorne and Verstappen, who took no part in the second segment of qualifying following his crash.
Raikkonen was top of the charts after the first runs, but his team mate Vettel in second had more time in hand after running very wide at the final turn.
Hamilton slotted into third, just a tenth off the pace, ahead of Bottas and Ricciardo with Gasly and Carlos Sainz in the Renault the only other drivers to set a banker lap, albeit on used supersoft tyres.
Vettel made no mistake on his second run, clocking the fastest first sector and personal bests in the next two to take pole. Raikkonen could not respond and will line up second.
Bottas popped into third, ahead of Hamilton, who will start Sunday’s race ninth and has never won a race from outside the top six.
Ricciardo was fifth quickest, two-tenths further back. Gasly was a sensational sixth, with Kevin Magnussen seventh for Haas. Hulkenberg, Force India’s Esteban Ocon and Sainz completed the top 10.