The German, who now holds a slender one-point advantage at the top of the Drivers' Championship standings, produced a stunning lap of 1:16.276 to set a new track record at the Hungaroring, while team-mate Kimi Raikkonen capped a good day for the Scuderia by qualifying second fastest.
He corrected that sharpish, clocking the quickest lap of the weekend so far to cruise through to Q3 on top of the pile - but pushed firmly by Vettel, around a tenth of a second behind.
Ferrari's German Sebastian Vettel, the 2017 Drivers Championship leader, one point ahead of Hamliton, lost control of his auto without crashing into the barriers, but managed to be sixth fastest with 1.077 seconds off the pace.
But here in Hungary things are a bit different, with a circuit perhaps more suited to the agile Ferrari than the power track Mercedes.
Ferrari have not taken a front row lockout in Hungary since 2004 - when victory secured the title for Michael SchumacherWhy have Mercedes fallen back?
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Memories of Monaco in May, where Ferrari romped to a one-two finish while Hamilton could manage only seventh, remained raw but Mercedes team boss Toto Wolff said the situation was not that dramatic. The three teams at the front seemed very close.
Though this doesn't tell much of his intentions after the season is over, it does give us insight into what has been an nearly completely drama-free relationship with Ferrari.
This was especially true in Qualifying, where Sebastian Vettel and Kimi Raikkonen took first and second place on the grid respectively, beating Bottas and Lewis Hamilton into third and fourth.
Triple World Champion Hamilton appeared to have his work cut out at a track where he was won five times before.
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"I definitively think that today, the whole day, Ferrari has been too quick for us", he said. It is just great work by the team, we have not brought many updates to the auto, we have just been able to exploit it a little more. "We're just hoping that we can be on our toes to react to whatever is thrown at us in the next races".
Germany's Sebastian Vettel received the flawless boost for the Formula One title race after seizing pole position in Hungary. We'll see. I think the race is long and a lot of things to look out for.
"We made a good step forward".
The damage to the Haas was so severe that Kevin Magnussen, whose auto Giovinazzi had been commandeered, was able to set just 11 laps after his mechanics finished repairing his vehicle late in free practice two.
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