Police announced via Twitter that Dzhokhar Tsarnaev was in custody. His brother, 26-year-old Tamerlan, was killed Friday in a furious attempt to escape police.
Dzhokhar Tsarnaev had been holed up in a boat in a Watertown neighborhood. The crowd gathered near the scene let out a cheer when spectators saw officers clapping.
"Everyone wants him alive," said Kathleen Paolillo, a 27-year-old teacher who lives in Watertown.
Boston Mayor Tom Menino tweeted "We got him," along with a photo of the police commissioner speaking to him.
During a long night of violence Thursday into Friday, the brothers killed an MIT police officer, severely wounded another lawman and hurled explosives at police in a car chase and gun battle, authorities said.
The suspects were identified by law enforcement officials and family members as Dzhokhar and Tamerlan Tsarnaev, ethnic Chechen brothers who had lived in Dagestan, which neighbors Chechnya in southern Russia. They had been in the U.S. for about a decade, an uncle said, and were believed to be living in Cambridge, Mass.
Tamerlan Tsarnaev, a 26-year-old who had been known to the FBI as Suspect No. 1 and was seen in surveillance footage of the marathon in a black baseball cap, was killed overnight, officials said. His younger brother, who had been dubbed Suspect No. 2 and was seen wearing a white, backward baseball cap in the images from Monday's deadly bombing - escaped and was on the run.
Their uncle in Maryland, Ruslan Tsarni, pleaded on live television: "Dzhokhar, if you are alive, turn yourself in and ask for forgiveness."
Authorities in Boston suspended all mass transit and warned close to 1 million people in the entire city and some of its suburbs to stay indoors as the hunt for Suspect No. 2 went on. Businesses were asked not to open. People waiting at bus and subway stops were told to go home. The Red Sox and Bruins postponed their games.
From Watertown to Cambridge, police SWAT teams, sharpshooters and FBI agents surrounded various buildings as police helicopters buzzed overhead and armored vehicles rumbled through the streets. Authorities also searched trains.
"We believe this man to be a terrorist," said Boston Police Commissioner Ed Davis. "We believe this to be a man who's come here to kill people."
The bombings on Monday killed three people and wounded more than 180 others, tearing off limbs in a spray of shrapnel and instantly raising the specter of another terrorist attack on U.S. soil.
Chechnya was 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.
Investigators in the Boston case have shed no light on the motive for the bombing and have said it is unclear whether it was the work of domestic or international terrorists or someone else entirely with an unknown agenda.
The endgame - at least for Suspect No. 1 - came just hours after the FBI released photos and video of the two young men at the marathon's finish line and appealed to the public for help in identifying and capturing them.
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 getaway attempt overnight.