Tamerlan Tsarnaev, 26, was wearing explosives and a triggering device when he died, a source briefed on the investigation told CNN on condition of anonymity.
The manhunt brought Boston to a near standstill. The Boston Red Sox announced they were postponing Friday night's game against the Kansas City Royals "to support efforts of law enforcement officers." NHL's Boston Bruins also postponed its game against the Pittsburgh Penguins.
The city's subway, bus, Amtrak train and Greyhound and regional Bolt Bus services were shut down. Taxi service across the city also was suspended for a time during the manhunt. Every Boston area school was closed.
Boston's public transit authority sent city buses to Watertown to evacuate residents while bomb experts combed the surroundings for possible explosives.
Initially, authorities said the brothers started their rampage by robbing a convenience store. By late Friday, the Middlesex District Attorney's office backtracked on the allegation, saying an investigation determined that the robbery at a 7-Eleven was unrelated.
The violent hours leading up to the capture began in Cambridge, across the Charles River from Boston, MIT officer Collier was shot and killed while he sat in his car on Thursday night, the Suffolk County District Attorney's Office said in a statement.
The two suspects, according to authorities, then hijacked a vehicle at gunpoint in Cambridge, telling the driver that they were the marathon bombers, a law enforcement source told CNN.
At some point, apparently at a gas station, that source said, the driver escaped.
Police, who were tracking the vehicle using its built-in GPS system, picked up the chase in Watertown. The pursuit went into a residential neighborhood, with the suspects throwing explosives at police.
A shootout erupted and ultimately one bomber -- later identified as Tamerlan Tsarnaev -- got out of the car. Police shot him, and his brother ran over him as he drove away, according to the law enforcement source, who spoke on condition of anonymity.
Richard H. Donohue Jr., 33, a three-year veteran of the transit system police force, was shot and wounded in the incident and taken to a hospital, a transit police spokesman said Friday. The officer's condition was not immediately known.
Another 15 police officers were treated for minor injuries sustained during the explosions and shootout, Jennifer Kovalich, a spokeswoman for St. Elizabeth's Medical Center, said.
Police believe the brothers are the same men pictured in images released Thursday by the FBI as suspects in the marathon bombing that killed three people and wounded dozens on Monday.
At least 58 people remained hospitalized, including three in critical condition, according to a CNN count.
The men are shown in the images walking together near the marathon finish line.
The first suspect -- apparently Tamerlan Tsarnaev, according to authorities -- appears in the images wearing a dark hat, sunglasses and a backpack. The second suspect, wearing a white cap, police said, is the one who remained at large throughout Friday until he was taken into custody Friday night.
But the mother of the Tsarnaev brothers refused to believe they were involved in the marathon bombings and subsequent shootout.
"It's impossible for them to do such things. I am really telling you that this is a setup," Zubeidat Tsarnaeva told state-run Russia Today from Dagestan.
"My son would never keep it in secret. ...If there is anyone who would know it would be me. He wouldn't hide it. But there was never a word."
The brothers came from the Russian Caucasus region and moved to Kazakhstan at a young age before coming to the United States several years ago.
"My youngest was raised from 8 years in America. My oldest was really properly raised in our house. Nobody talked about terrorism," their mother said.
The suspects' parents recently returned to Dagestan in the Caucasus region after living in the United States for about 10 years because they were "nostalgic," the father, Anzor Tsarnaev, told Russian state-run Zvezda TV.
He accused someone of framing his sons. "I don't know who exactly did it. But someone did."
A federal official told CNN that Dzhokar Tsarnaev came to the U.S. as a tourist with his family in the early 2000s and later asked for asylum. He became a naturalized U.S. citizen in 2012. Tamerlan Tsarnaev was not a naturalized citizen, said the official, who spoke on condition of anonymity. He came "a few years later" and was lawfully in the United States as a green-card holder.
Tamerlan Tsarnaev had studied at Bunker Hill Community College and wanted to become an engineer, according to those who knew him. He then took a year off to train as a boxer.