Four-times world champion Vettel ended the session in 12th, 1.602 seconds behind Bottas, after withdrawing early due to "a loss in the hydraulic pressure circuit".
Fresh from a glorious season-saving triumph at one of his favourite venues, Lewis Hamilton sets out to tame his unpredictable and sometimes wayward "diva" of a Mercedes again as the Formula One circus endures sizzling heat at the Azerbaijan Grand Prix. The Ferraris and the Red Bulls were quick on to the track, but a Mercedes was the quickest around it - Lewis Hamilton leading the way.
Bottas's teammate, Hamilton, said in Baku: "I honestly think he has earned his place with us".
The Force India driver took too much kerb on entry, pitching the auto into the wall on the exit and causing significant damage to the front-right corner. "He is coping so well with the hard days".
Fellow Formula One title rival Sebastian Vettel was only 12th fastest and did not partake in the final 25 minutes of running after a hydraulic issue, but Ferrari expects Vettel's vehicle to be ready for this afternoon's qualifying session. "This is what the very best are made of".
Vettel, who is gunning for a fifth F1 title, also appears to be No. 1 at Ferrari ahead of Kimi Raikkonen.
But Ferrari are mounting the biggest challenge yet to that monopoly, with three wins to Mercedes' four so far this term.
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The 6-kilometer (3.7-mile) circuit glides through the city's medieval walls and passes the Caspian sea.
Although his Ferrari team managed to resolve the failure in time for qualifying, Vettel was only fourth and 1.3 secs slower than Hamilton.
During last year's Baku qualifying, Bottas, then with Williams, registered the highest speed ever recorded in a Formula One session, reaching 373 km/h (234 mph) on what is the longest stretch of any race on the calendar.
Vettel showed all his mettle in Canada, however, when he started on the front row, dropped to last and came back through the field to fourth with a fighting display that earned him the Driver of the Day award.
McLaren are in their third year of a long-term contract with Honda, but are the only team without a single point to their name this season following a awful start to the new campaign.
Fernando Alonso (Spain) McLaren 1:47.551 18.
He can hardly even finish a race these days, such is the unreliability of McLaren's Honda engine.
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