The Coast Guard started towing the "Overseas Reymar" out of the bay a little after 10 a.m. Friday. The oil tanker has been anchored near Treasure Island since the collision.
The Coast Guard said it has completed safety inspections and finished collecting evidence.
The tanker has to be repaired before it can carry oil again.
On Thursday the Harbor Safety Committee agreed to study a new safety plan to limit the number of vessels around the bay bridge when visibility is low.