The shutdown came hours after the killing of one suspect, known as the man in the black hat from marathon surveillance footage.
All modes of public transportation were shut down, including buses, subways, trolleys, commuter rail and boats, said Joe Pesaturo, spokesman for the Massachusetts Bay Transportation Authority.
The suspects' clashes with police began only a few hours after the FBI released photos and videos of the two young men, who were seen carrying backpacks as they mingled among marathon revelers. The bombings on Monday killed three people and wounded more than 180 others, and authorities revealed the images to enlist the public's help finding the suspects.
The images released by the FBI depict two young men, each wearing a baseball cap, walking one behind the other near the finish line. Richard DesLauriers, FBI agent in charge in Boston, said the suspect in the white hat was seen setting down a bag at the site of the second of two deadly explosions.
Authorities said surveillance tape recorded late Thursday showed the suspect known for the white hat during a robbery of a convenience store in Cambridge, near the campus of MIT, where a university police officer was killed while responding to a report of a disturbance, said State Police Col Timothy Alben. The officer died of multiple gunshot wounds.
From there, authorities say, the two men carjacked a man in a Mercedes-Benz, keeping him with them in the car for half an hour before releasing him at a gas station in Cambridge. The man was not injured.
The search for the vehicle led to a chase that ended in Watertown, where authorities said the suspects threw explosive devices from the car and exchanged gunfire with police. A transit police officer was seriously injured during the chase, authorities said.
In Watertown, witnesses reported hearing multiple gunshots and explosions at about 1 a.m. Friday. Dozens of police officers and FBI agents were in the neighborhood and a helicopter circled overhead.