Crabtree finished with a game-high 109 receiving yards and a touchdown in the loss.
Raven's quarterback Joe Flacco won MVP honors with 287 passing yards and three touchdowns.
Baltimore led 28-6 early in the third quarter when a power outage delayed the game for more than 30 minutes.
When play resumed the 49ers scored 17 points in just over four minutes to pull within five points.
San Francisco had a chance to take the lead in the final two minutes but failed to convert on 4th and goal when Colin Kaepernick's pass to Crabtree sailed out of bounds.