After completing his last lap of the session, Verstappen overtook Hamilton at the top of the timesheets, pulling 0.313 seconds ahead of the seven-time world champion.
Sergio Perez of Red Bull also turned in the quickest time on his last lap, climbing to third position 0.376 seconds behind the leader.
Lando Norris of McLaren, Verstappen’s closest title rival, finished fourth, 0.481 seconds behind the Dutchman.
Charles Leclerc of Ferrari, who had been consistently fastest in the first half of the session until he skidded straight on at Turn 15 halfway through, was the cause of one of the red-flag stoppages.
Although Leclerc’s Ferrari’s front suspension was broken, it should be able to be repaired in time for the second session, which starts at 14:00 BST.
Debris on the track prompted the first red flag period, and the Argentine Franco Colapinto’s collision in the Williams produced the last one.
Carlos Sainz of Ferrari finished fifth fastest, followed by Oscar Piastri of the second McLaren, Fernando Alonso of Aston Martin, George Russell of Mercedes, and Leclerc, whose pace on medium tires prior to his crash was still good enough for ninth place.
The cars in front of him were all running on soft tires.At this early stage, Verstappen and Red Bull seemed more fit than they did during a challenging weekend at the Italian Grand Prix the previous time around.