Stroll's performance was a welcome boost to a Racing Point team reeling from seeing fellow driver Sergio Perez sidelined from the race after testing positive for coronavirus.
Verstappen set a fastest lap time of 1m27.422s on the soft compound tyre to finish 0.474 seconds clear of Hamilton, who set his best lap on mediums in the leading Mercedes.
Verstappen set the pace in the morning session by a comfortable margin of nearly half a second over Mercedes' Lewis Hamilton.
On the long runs we also looked quite decent but who knows what the weather will be like for the rest of the weekend and how that will change things! "We expected worse coming into today but the vehicle feels good and it was hooked up straight away from the first lap in FP1. I'm sure Mercedes are hiding quite a lot but as a auto it feels well balanced".
The German acquitted himself well, setting the ninth best time despite reporting some discomfort from the seat - and having to wear his team-mate Lance Stroll's spare overalls.More news: Teenager arrested for masterminding Twitter hack
Mercedes have won all three races so far this year.
"It has been quite a hard day", he said.
"Yesterday (Friday), for example, it was really tricky in the low-speed corners, but today, the wind changes and it becomes like a completely different auto, luckily in the right way, because today was a lot more fun to drive". The balance is not as good as I'd like.
Leclerc was Ferrari's sole runner for most of the session after teammate Sebastian Vettel was only able to complete two laps due to an issue with the intercooler on his SF1000 auto.
The German was then 18th after lunch, when Ferrari chose to change his car's pedals.More news: How Michigan MAC schools are impacted by SEC’s conference-only football schedule
Hamilton, in imperious form at the last two races, is bidding for a record-increasing seventh home win at Silverstone tomorrow.
"It's been a special, insane and wild 24 hours, but it's all worth it", said the German driver.
"He's certainly being thrown in at the deep end, but he's a fast learner and I'm sure he will get up to speed quickly".
Alfa Romeo driver Antonio Giovinazzi brought out a red flag less than 30 minutes into the session following a spin at the exit of Becketts, causing him to flat-spot all four tyres and damage the floor of his vehicle.
Formula One said Perez was the sole positive from the latest batch of 3,909 tests carried out between July 24-30.More news: Boston Marathon death sentence overturned at appeal