The Canadian driver posted a 1m27.274s to top the times from Red Bull's Alex Albon, who finished second despite crashing into the barriers.
Albon forced the session to be red-flagged after he lost control of his car at Stowe, causing heavy damage to his Red Bull RB16.
Valtteri Bottas was the quickest Mercedes driver in third as the German squad enjoyed a subdued session.
Teammate Lewis Hamilton wound up fifth behind the Ferrari of Charles Leclerc.
The Ferrari driver's teammate Sebastian Vettel lost more track time after not doing any running in FP1. Vettel finished down in 18th position after his team had to change the pedals of his car.
F1 returnee Nico Hulkenberg was seventh quickest in the second Racing Point, six tenths off Stroll's pace.
Full report to follow