The championship leader topped the charts by 0.4 seconds from team-mate Sergio Perez, clocking 1 minute 27.901 seconds, the fastest time of the weekend so far.
Verstappen topped the timesheets on his first flying lap, a 20-minute run, setting a 1m28.541s to undercut the then-leading Leclerc.
He continued to improve, first to 1m28.498s before dropping a further 0.15s with purple sector two.
Despite improvements across the field, no one could match the Dutchman’s time, with a late challenge from Leclerc falling 0.002 seconds short before Verstappen improved again.
The Monegasque driver had to finish second before Perez climbed from sixth to second, although he was still 0.4s clear of his team-mate, dropping the Ferrari man to third.
Mercedes home favorites George Russell and Lewis Hamilton finished fourth and fifth respectively, also showing promising pace in Friday’s only dry practice session.
Aston Martin was first on track, with Sebastian Vettel and Lance Stroll looking to take advantage of the second dry session of the weekend after Friday’s FP1 was interrupted by rain.
Alpine’s Fernando Alonso was the first to clock a time on the board with a 1m34.826s before team-mate Esteban Ocon brought him down by going 1.8s quicker on his first attempt.
The McLarens of Daniel Ricciardo and Lando Norris were next with quick times, swapping top spot before Leclerc took the lead with a 1m29.452s – the first sub-1m30 time of the weekend.
Sainz was next to set a flying lap, but settled for second place, reporting difficulties in high-speed sections of the track.
With 10 minutes into the session, the timing board resembled a scene from Noah’s Ark, with the teams taking positions two by two, Ferrari leading Alfa Romeo, McLaren and Alpine.
Perez was the first of the Red Bulls to complete a representative lap, splitting the Ferrari pair with a 1m29.629s, 0.17s behind Leclerc.
Russell’s first attempt was only good enough for 10th, but Hamilton took third at the start to push Sainz into fourth.
Perez briefly improved to top the grid, but Leclerc took the lead again with 20 minutes to spare, clocking 1m29.021s.
Verstappen then took the lead, where he stayed for the rest of the session, repeatedly improving his time to seal first place ahead of qualifying.
Russell improved to fourth with 15 minutes remaining with a 1m28.426s, pipping Hamilton to fifth in a race he has won eight times.
Several drivers battled at Turn 3, with Vettel, Perez and Sainz running wide in the Village during the hour-long practice session.
Sainz settled for sixth after his struggles despite leading FP2 on Friday, with Norris seventh.
Valtteri Bottas (Alfa Romeo), Mick Schumacher’s Haas and Alonso round out the top 10.
AlphaTauri endured another difficult session, with Pierre Gasly and Yuki Tsunoda finishing 15th and 17th after the Frenchman said Silverstone had exposed their car’s weakness in high-speed corners.
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