The desert track's warmer temperatures and longer straights most likely played to the Scuderia's strength, but that should take nothing away from Vettel, who beat teammate Kimi Raikkonen to pole position by 0.143s.
Raikkonen had escaped a grid penalty of his own as he clocked a best lap time of one minute and 29.817 seconds to outpace four-time champion Vettel by 0.011 seconds.
His hopes of chalking up a third Bahrain win on Sunday have already taken a hit, with the Briton set to drop five places on the grid for an unscheduled gearbox change on his Mercedes.
"Overall I have been happier this weekend with how the auto has been responding and how the front end is responding".
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A mistake at the last corner on his first run in the top 10 shoot-out left Vettel second but a blistering final lap gave him pole ahead of Raikkonen by 0.143secs.
Vettel will want the honours to continue coming in, and while he won last week, the Ferrari star will be wary of a Mercedes team that will want to storm back. Really happy that I got the second run and got it clean.
Vettel admitted after winning the season opener in Australia that his team still needed to make improvements to the SF71H, so F1 rivals Mercedes came into Bahrain favourites after Lewis Hamilton's dominant Q3 performance in Melbourne. It looked like a similar error, just losing control of the vehicle through the apex, at a race Red Bull would have hoped to have two cars putting Ferrari under pressure from the very start.
Raikkonen, who showed impressive pace during the weekend's three practice sessions, had been ahead after the initial attempts in the top-ten qualifying shootout and had the advantage of being the last man to start his final run.
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The two Red Bulls of Verstappen and Daniel Ricciardo followed behind in second and third respectively.
"But after the weekend, after the race distance, when you have so many laps - I had a very good understanding and feel, and we have been talking about it and looking into it". "In clear air we were actually very, very strong", the 28-year-old told reporters.
And the race, scheduled for Sunday, starts at twilight and finishes under lights in order to avoid most of the heat of the day.
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More than 451 athletes have applied for a place. "She asked loads about me". She also opted for an olive green trench coat from Babaton by Aritzia.
Such support came as no surprise given their performances on the track, Williams finding it particularly hard as Lance Stroll and Sergey Sirotkin finished FP2 17th and 18th respectively.