The Mercedes duo of Valtteri Bottas — fastest in the first session — and defending champion Lewis Hamilton ranked fourth and fifth, respectively, in the second practice.
Ferrari driver Kimi Raikkonen was the second quickest in both sessions, and in the afternoon he was only 0.007 behind Hamilton.
Vettel was almost overtaken by Bottas on the last lap, but made a crucial blocking move and won by only 0.6 seconds.
World champion Lewis Hamilton could only manage fourth, and will start from ninth on Sunday after incurring a grid penalty.
Raikkonen and Vettel were up front as cooler temperatures and nightfall matched the conditions for Sunday evening's race. Raikkonen's time of 1 minute, 29.8 seconds on the 5.4-kilometer (3.3-mile) desert circuit was a fraction quicker than Vettel's.
Raikkonen currently sits fifth in the driver's standings heading into this weekend's season-ending Abu Dhabi Grand Prix.
Despite Ferrari's status as Formula One's richest and most popular team, it hasn't won a driver's championship since Kimi Raikkonen in 2007.
The Finish driver refused to give up on Ferrari's season and stressed that his team is still capable of clinching victories in remaining four races of the season.
Having seen both of its cars fail to score points at the previous race in Singapore, Ferrari lost Kimi Raikkonen moments before this race.
Vettel, meanwhile, was handed a 20-place grid penalty after Ferrari made several component changes to his engine before the race.
It was a reversal of Friday's second practice when Vettel was quickest ahead of Raikkonen.
Raikkonen is fifth in the 2017 drivers' standings with 138 points, while Vettel is in the second spot with 235 points, 28 behind leader Hamilton.
Raikkonen lies at the fifth spot in the drivers' championship, 86 points behind teammate Sebastian Vettel, who leads the current standings.
Red Bull's Max Verstappen was fourth, followed by Hamilton's teammate Valtteri Bottas and Raikkonen's teammate Sebastian Vettel.
Lewis Hamilton wins a record-equalling fifth British Grand Prix as Sebastian Vettel finished seventh after suffering a late puncture in the penultimate lap.
Lewis Hamilton's 66th pole moves him one ahead of Formula One great Ayrton Senna and just two behind Michael Schumacher's all-time record of 68.
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