Police said three other people were taken into custody for questioning at an off-campus housing complex at the University of Massachusetts Dartmouth where the younger man may have lived.
"Tonight, our family applauds the entire law enforcement community for a job well done, and trust that our justice system will now do its job," said the family of 8-year-old Martin Richard, who died in the bombing.
Queries cascaded in after authorities released the surveillance-camera photos — the FBI website was overwhelmed with 300,000 hits per minute — but what role those played in the overnight clash was unclear. State police spokesman Dave Procopio said police realized they were dealing with the bombing suspects based on what the two men told a carjacking victim during their night of crime.
The search by thousands of law enforcement officers all but shut down the Boston area for much of the day. Officials halted all mass transit, including Amtrak trains to New York, advised businesses not to open and warned close to 1 million people in the city and some of its suburbs to unlock their doors only for uniformed police.
Around midday, the suspects' uncle, Ruslan Tsarni of Montgomery Village, Md., pleaded on television: "Dzhokhar, if you are alive, turn yourself in and ask for forgiveness."
Until the younger man's capture, it was looking like a grim day for police. As night fell, they announced that they were scaling back the hunt and lifting the stay-indoors order across the region because they had come up empty-handed.
But then the break came and within a couple of hours, the search was over. Dzhokhar Tsarnaev was captured about a mile from the site of the shootout that killed his brother.
A neighbor described how heavily armed police stormed by her window not long after the lockdown was lifted — the rapid gunfire left her huddled on the bathroom floor on top of her young son.
"I was just waiting for bullets to just start flying everywhere," Deanna Finn said.
When at last the gunfire died away and Dzhokhar Tsarnaev was taken from the neighborhood in an ambulance, an officer gave Finn a cheery thumbs-up.
"To see the look on his face, he was very, very happy, so that made me very, very happy," she said.
Authorities said the man dubbed Suspect No. 1 — the one in sunglasses and a dark baseball cap in the surveillance-camera pictures — was Tamerlan Tsarnaev, while Suspect No. 2, the one in a white baseball cap worn backward, was his younger brother.
Chechnya, where the Tsarnaev family has roots, has been the scene of two wars between Russian forces and separatists since 1994, in which tens of thousands were killed in heavy Russian bombing. That spawned an Islamic insurgency that has carried out deadly bombings in Russia and the region, although not in the West.
The older brother had strong political views about the United States, said Albrecht Ammon, 18, a downstairs-apartment neighbor in Cambridge. Ammon quoted Tsarnaev as saying that the U.S. uses the Bible as "an excuse for invading other countries."
Also, the FBI interviewed the older brother at the request of a foreign government in 2011, and nothing derogatory was found, according to a federal law enforcement official who was not authorized to discuss the case publicly and spoke on condition of anonymity.
The official did not identify the foreign country or say why it made the request.
Exactly how the long night of crime began was unclear. But police said the brothers carjacked a man in a Mercedes-Benz in Cambridge, just across the Charles River from Boston, then released him unharmed at a gas station.
They also shot to death a Massachusetts Institute of Technology police officer, 26-year-old Sean Collier, while he was responding to a report of a disturbance, investigators said.
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