After Friday's two practice sessions went off in dry conditions, the rain fell at Spa giving the drivers and their teams little chance to prepare for qualifying later on Saturday.
Stroll aquaplaned after the Raidillon corner and spun off hitting the barriers, breaking the left-front suspension of his Aston Martin, and the red flag came out after only 12 minutes of the session.
"Lance had an incident in the rain in FP3. He got out of the car unaided and has been taken by the medical car to the medical centre for routine precautionary checks," Aston Martin said.
Verstappen was out early and posted a time of two minutes and 01.565 seconds, almost 20 seconds slower than the fastest time by Lando Norris on Friday, but nobody could improve upon the Dutchman's time in the poor conditions.
Three drivers, Ferrari's Carlos Sainz, George Russell of Mercedes and Haas' Kevin Magnussen, had not even made it onto the track before the red flag was waved after Stroll's crash.
The green flag did come out briefly, but nobody ventured out of the garages, and the red flag again put an end to anyone's chances of some final work before qualifying as the rain continued, leaving plenty of water on the track.
The session did resume for the final two minutes of the session, to allow drivers practice their starts, and they will now hope conditions improve before qualifying starts.
McLaren's Oscar Piastri, winner of his first F1 GP at Hungary last weekend, had the second fastest time, 1.433 seconds down on Verstappen, with Alpine's Pierre Gasly third and Piastri's teammate Norris fourth.
Norris is second in the drivers' championship, 76 points behind Verstappen, and his performance on Friday showed he will be a threat to the leader this weekend, who will face a 10-place grid penalty after Red Bull took on a fifth engine.
Esteban Ocon of Alpine was fifth fastest, ahead of Ferrari's Charles Leclerc, with Stroll in seventh.
"Lance is back in the team's hospitality and is ok. The team will now work on repairing the damage to his AMR24 ahead of qualifying," Aston Martin said.
Sauber's Valtteri Botas was eighth fastest, with Mercedes' Lewis Hamilton ninth and Red Bull's Sergio Perez 10th, 5.538 seconds down on his teammate.