The boy and three juvenile accomplices allegedly attempted to break into about 10 city vehicles parked behind City Hall on Santa Clara Street, police Sgt. Jeff Bassett said.
An anonymous caller reported the break-ins, which resulted in several broken windows and damage to toolboxes.
Officers responded and spotted the four suspects, who ran, Bassett said. Officers caught two of the boys, a third got away, and a fourth ran toward the ferry terminal before jumping into the water around 3:45 a.m.
Police lost sight of the boy and called the U.S. Coast Guard to assist in the search.
A Coast Guard boat from the Vallejo station and a search helicopter were deployed, Coast Guard petty officer John Eastman said.
The boy was found under a pier around 5 a.m., Bassett said.
"He was pretty cold, as you can imagine," he said.
He was transported to a hospital as a precaution and was arrested, Bassett said.
A vehicle the boy allegedly drove prior to jumping in the water had been reported stolen, so he will also face charges of stealing that vehicle, Bassett said.
The other two juveniles arrested for the break-ins will face charges of vehicle burglary, and the fourth suspect is still at large, Bassett said.