The suspect "was severely injured in most likely the shootout that occurred" overnight Thursday, though he may also have been hurt in an exchange of gunfire Friday night in Watertown, a Boston suburb, CNN reported citing police Commissioner Ed Davis.
The dramatic capture of Dzhokar Tsarnaev came after a Watertown resident saw blood on a boat in his neighbour's backyard, Davis said. "He opened the tarp and saw a man covered in blood," he said. The man retreated and alerted law enforcement.
Despite being bloody, the suspect exchanged gunfire with authorities from his hiding place, Davis said. Tsarnaev did not have explosives on him at the time of capture, according to Davis.
Law enforcement officials erupted in cheers in Watertown Friday night moments before Boston police tweeted that the second suspect was in custody, CNN said.
Earlier officials repeatedly appealed for surrender by Tsarnaev. Using a bullhorn they said: "We know you're in there" and "Come out with your hands up."
Dzhokar Tsarnaev was on the run after escaping a shootout with police that left his older brother Tamerlan Tsarnaev, 26, dead.
The two brothers of Chechen origin, from the disputed Muslim region of Chechnya in Russia, but who were born in Kyrgyzstan, are reported to have come to the US a decade ago.
The younger one became an American citizen last year Sep 11, NBC News reported citing a law enforcement official.
Meanwhile, the FBI took two males and a female into custody for questioning Friday evening at a New Bedford, Massachusetts, residence believed to have been connected to the younger suspect.
FBI agents interviewed Tamerlan Tsarnaev in 2011 at the request of a foreign government, CNN said citing an FBI official.
The other government - who the official would not name - suspected that Tsarnaev may have ties to extremist groups.
The FBI investigated, including interviewing Tsarnaev, but the matter was closed after no derogatory information was found, according to the official.