Hamilton had completed fifteen laps in his W04 when he came off the track at the Dry Sac corner in Jerez, damaging the front of his car.
"Lewis suffered a loss of rear brake pressure, the front brakes enabled him to slow the car but he couldn't avoid the barrier..." Mercedes posted on Twitter.
After a couple of hours of investigating the problem, the team added "we have traced the problem to the hydraulic brake line connecting to the right-rear caliper."
Nico Rosberg will drive the car tomorrow. The German completed only eleven laps on Tuesday when an electrical fault caused a fire in his W04.