Boston police announced the arrest of Dzhokhar Tsarnaev, 19, on their Twitter account: "CAPTURED!!! The hunt is over. The search is done. The terror is over. And justice has won. Suspect in custody."
Shortly after, the department sent another tweet, urging people in their "time of rejoicing" to not forget the families of those allegedly killed by the suspect and his brother, who died earlier.
The Boston Globe reported Tsarnaev was apprehended after being cornered in a boat in the back yard of a Watertown home. Police used "flash bang" stun grenades to disorient and distract the man, the newspaper said, and the police sources said an ambulance was sent to the scene.
Scores of people lined both sides of the street and cheered the law enforcement personnel as they drove away.
Upon learning of the arrest, Boston Mayor Thomas Menino tweeted: "Your mayor is very proud of you."
The Boston Globe reported the suspect was rushed to a local hospital. A state official said the suspect was "alive, conscious, captured."
In another development, the Globe said New Bedford police said two men and a women who are were taken into custody in that city as part of the bombing investigation. The trio may have been students at the University of Massachusetts where Tsarnaev was a student.
Tsarnaev's arrest came after shots were fired within an hour after police said residents could leave their homes following an all-day lockdown and door-to-door search.
NBC said dozens of police and armored vehicles converged on the location where the shooting was heard and residents were ordered to take shelter as officers cordoned off the area.
Massachusetts State Police Col. Timothy Alben described Tsarnaev as "a very violent and dangerous person."
Tsarnaev and his brother Tamerlan, 26, were named as suspects in Monday's explosions at the finish line of the Boston Marathon, that killed three people and injured more than 170. Thursday night, the brothers allegedly killed a Massachusetts Institute of Technology police officer and critically wounded a Massachusetts Bay Area Transit officer, then engaged in a shootout with police in Watertown that left the elder brother dead. WCVB-TV, Boston, said Dzhokhar Tsarnaev ran over his brother as he fled the scene.
Gov. Deval Patrick told a late afternoon briefing the lockdown imposed on Watertown had been lifted and people were allowed outside their homes. The suspension of public transportation also was lifted.
Alben told the same briefing the search of the neighborhood where the shootout occurred was "not fruitful" but pledged, "We remain committed to this. We do not have an apprehension but we will have one."
Alben said Tsarnaev had abandoned his vehicle and fled on foot, triggering the lockdown and search in a 20-block area.
WCVB said police found homemade explosives, pipe bombs and a pressure cooker in their search of the shootout scene as well as 200 rounds of spent ammunition.
"[We found] unexploded ordnance that were made safe and removed," Alben said.
Cambridge mechanic Gilberto Junior said Dzhokhar Tsarnaev came into his shop Tuesday, seeking his girlfriend's car, a white Mercedes wagon, even though it had yet to be repaired.
"He was very nervous. He was biting his fingernails and shaking his legs," Junior told WCVB. "He was very agitated.
"I wish I knew at the time it was him."
Alben said he had no knowledge of a white Mercedes associated with the suspect.
Police said the brothers shot and killed MIT police officer Sean Collier, 26, of Somerville and critically wounded Massachusetts Bay Area Transit officer Richard Donahue Jr., 33. Donahue was reported in stable condition following surgery.
The Globe reported an explosive trigger was found on Tamerlan's body, which exhibited "blast wounds," when it was examined at the morgue.
Before the shootout, police said the suspects tossed a pressure cooker bomb at their pursuers -- similar to the devices that exploded Monday.
Boston media reported Dzhokhar Tsarnaev became a U.S. citizen last Sept. 11.
Ruslan Tsarni, an uncle of the suspects, said he was ashamed of his nephews.
"I never would have imagined the children of my brother would have been involved in that," he said.
Tsarni, who said his family was ethnic Chechen and Muslim, said his nephews "put a shame on our family. He put a shame on entire Chechen ethnicity."
NBC News reported counterterrorism officials were looking into the possibility the Tsarnaev brothers were linked to the Islamic Jihad Union of central Asia, a terrorist group. NBC New York said it had obtained travel records indicating Tamerlan Tsarnaev went to Russia from Jan. 12-July 17, 2012.
The men's father, Anzor Tsarnaev, told the Los Angeles Times in a telephone interview from his home in Dagestan he does not believe his sons were involved in the events.
"It is a provocation of the special services who went after them because my sons are Muslims and don't have anyone in America to protect them," said the elder Tsarnaev, adding his boys had no training in handling firearms or explosives.
"I'm hurt for everyone who has been hurt. I'm sorry for all the people who are hurt and for all the people who lost their lives," the men's sister, who lives in West New York, N.J., and whose name was withheld, told The (Newark, N.J.) Star-Ledger.
She said she never would have expected her brothers to be involved in such violence.
After their photos were released by the FBI Thursday, the brothers carjacked a Mercedes sport utility vehicle and told the driver they were behind Monday's attack and had just killed a campus security officer, a source told NBC News. The driver was released unhurt.