The Briton, who has joined the team from McLaren, had been third quickest in the morning when, after 15 laps, he ran off the track at the Dry Sack hairpin.
Television footage of the incident showed he had locked up in the braking area of the corner, before skipping across the gravel trap and nosing into the barriers.
Hamilton was able to climb out of the car unaided, and returned to the pits.
Damage to the car appeared to be limited to the front wing and front suspension, and Mercedes is likely to be able to get it repaired for later in the day.
There was no initial answer from the team as to whether the accident had been caused by a mechanical problem or driver error.
The setback comes just 24 hours after Mercedes' first day of running was also cut short when team-mate Nico Rosberg was stopped on track with an electrical problem.
Revisions to the team's wiring loom were required overnight, which meant Rosberg had been unable to resume running during the afternoon session.
Despite the reliability disappointment, Rosberg had still been encouraged by what he had experienced with the car.