Dzhokhar Tsarnaev, aged 19, was found hiding in a boat in the backyard of a house in the Boston suburb of Watertown, wounded and weary after a gun battle with police overnight in which his accomplice brother was killed.
Boston Police Commissioner Ed Davis said that with Tsarnaev's arrest, "the citizens of the city of Boston and this area can be confident that the threat has been removed".
Police, state troopers and FBI agents zeroed in on the boat on Franklin Street after a man went out of the house and saw blood on the boat, Davis said.
The man then opened the tarp covering the boat and saw a man covered with blood inside, and called police.
"I'm so happy because the people in the greater Boston area will be able to sleep tonight because of the work of these individuals," Boston Mayor Thomas Merino told reporters, in a tribute to police and law enforcement agencies.
200 rounds of fire exchanged
Davis said a perimeter was set up around the boat before a major operation ended a drama that started with the twin bombing at the marathon on Monday.
"Over the course of the next hour or so, we exchanged gunfire with the suspect who was inside the boat," he said.
"And ultimately, the hostage rescue team of the FBI made an entry into the boat and removed the suspect who was still alive in the boat."
The two main suspects in the bombings that killed three people and wounded about 180 others - Tsarnaev and his older brother Tamerlan - were located after a police officer was killed and another wounded during a violent spree overnight that began at the Massachusetts Institute of Technology's campus.
Davis said more than 200 rounds of gunfire were exchanged during that incident, and that the two men had hurled improvised explosive devices and handmade hand grenades at officers.
The 26-year-old elder brother died of bullet wounds and injuries from explosives strapped to his body, a hospital doctor said.