Italian Antonelli, 19, clocked a best time of 01:45.990 seconds, 0.139s quicker than McLaren's reigning world champion Lando Norris.
Red Bull's Max Verstappen was third on the timesheets with Antonelli's teammate and closest title rival George Russell fourth.
Hamilton was fifth fastest but left his mechanics with a race against time to repair the car after he went off into the gravel at Fagnes and clouted the tyre wall, smashing the rear wing and suspension and sending debris across the track as the car bounced in the air.
"I've destroyed the car, mate. I'm sorry," the seven-time world champion told his race engineer over the team radio, before getting out and inspecting the damage.
"No problem," replied his race engineer Carlo Santi.
Verstappen slowed for double yellow flags after the accident and Williams' Carlos Sainz almost ran into the back of his car.
Ferrari's Charles Leclerc was sixth fastest, ahead of McLaren's Oscar Piastri and Audi pair Nico Hulkenberg and Gabriel Bortoleto with Red Bull's Isack Hadjar completing the top 10.