"Everyone wants him alive," said Kathleen Paolillo, a teacher.
Boston Mayor Tom Menino tweeted, "We got him."
Police said three other people were taken into custody for questioning at an off-campus housing complex at the University of the Massachusetts at Dartmouth where the younger man may have lived.
Up 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 because they had come up empty-handed.
But then a break came in a Watertown neighborhood when a homeowner saw blood on his boat, pulled back the tarp and saw the bloody suspect inside, police said.
Chechnya has been the scene of two wars between Russian forces and separatists since 1994, and 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 neighbor in Cambridge. Ammon quoted Tsarnaev as saying that the U.S. uses the Bible as "an excuse for invading other countries."
The search for the younger brother all but paralyzed the Boston area for much of the day. Officials shut down 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 stay inside and unlock their doors only for uniformed police.
"We believe this man to be a terrorist," Boston Police Commissioner Ed Davis said. "We believe this to be a man who's come here to kill people."
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."