Nineteen-year-old Dzhokhar Tsarnaev, an ethnic Chechen and reportedly a naturalized American citizen, was said to have been taken to an area hospital in serious condition.
The news came shortly after blasts and gunfire were reported at the center of a massive dragnet established to corral the younger of the two men thought by authorities to have perpetrated the April 15 attack.
U.S. President Barack Obama said "an important chapter in this tragedy" had been closed.
"Boston police, and state police and local police across the Commonwealth of Massachusetts responded with professionalism and bravery over five long days. And tonight because of their determined efforts, we've closed an important chapter in this tragedy."
Obama said questions, however, remain.
"Obviously tonight there are still many unanswered questions. Among them: Why did young men who grew up and studied here as part of our communities and country resort to such violence? How did they plan and carry out these attacks, and did they receive any help? The families of those killed so senselessly deserve answers."
"The Boston Globe" said Tsarnaev was apprehended a little after 8:45 p.m. local time. It quoted a state official saying the suspect was "alive, conscious, captured."
Boston's mayor tweeted simply "We got him," and later told reporters at a police press conference, "The people of greater Boston will be able to sleep tonight."
On its Twitter feed, the Boston police department announced, "The hunt is over. The search is done. The terror is over. And justice has won. Suspect in custody."
Reports had quoted official sources suggesting shortly before news of the capture that Tsarnaev was "pinned and alive," possibly in a boat stored in the backyard of a Watertown home.
Reports claimed police had been tipped off by a resident who saw what looked like blood on the boat.
Dzhokhar Tsarnaev's 26-year-old brother and fellow suspect in the bombings, Tamerlan, was killed in a shoot-out with police in the early hours of April 19.
The two are believed to have shot and killed a campus police officer at the nearby Massachusetts Institute of Technology (MIT).
A transit police officer was left seriously wounded in a gunbattle as authorities closed in on them.
The breakthrough came at the end of a tense day in and around Boston, and just an hour or so after police announced that they were scaling back the hunt because they had come up empty-handed following an all-day search that sent thousands of SWAT team officers into the streets and paralyzed the metropolitan area.
The city had been in a near-complete lockdown since the gunbattle that killed the elder Tsarnaev, allegedly after they killed the campus police officer and carjacked an automobile and were reportedly at a convenience-store robbery.
Three people were killed and 176 others injured -- many of them seriously -- in the April 15 dual bombing near the finish line of the storied Boston Marathon. The dead include an 8-year-old boy, a Chinese graduate student, and a young restaurant manager.
It was the worst terror attack on U.S. soil since the Al-Qaeda attacks with hijacked passenger airliners on September 11, 2011 killed nearly 3,000 people.
A U.S. government official said the FBI interviewed Tamerlan Tsarnaev at the request of an unidentified foreign government in 2011 but that nothing suspicious had been found.
U.S. President Barack Obama discussed the Boston bombings with Russian President Vladimir Putin in a telephone call on April 19.
According to a White House statement, Putin offered condolences over the Boston bomb attacks and the two leaders pledged to continue "cooperation" on counterterrorism and security going forward.
Tamerlan Tsarnaev was born in Tokmok, Kyrgyzstan, and Dzhokhar was born in the southern Russian republic of Daghestan, according to a relative interviewed in Tokmok by RFE/RL's Kyrgyz Service.