Officials said Tsarnaev, 19, and his older brother set off the twin explosions at last week’s race that killed three people and wounded more than 180.
His brother, Tamerlan, 26, died on Friday after a fierce gunbattle with police.
Tsarnaev was listed in a serious but stable condition at Beth Israel Deaconess Hospital, unable to speak because of a gunshot wound to the throat. It was not clear whether Tsarnaev was shot by police or inflicted the wound himself.
After an all-day manhunt that brought the Boston area to a near-standstill, he was captured on Friday night, wounded and bloody, after he was discovered hiding in a tarp-covered boat in a Watertown backyard.
The charges represented a decision by the Obama administration to prosecute him in the federal court system instead of trying him as an enemy combatant in front of a military tribunal. Under the military system, defendants are not afforded some of the usual US constitutional protections.
Tsarnaev, an ethnic Chechen from Russia who has lived in the US for about a decade, is a naturalised US citizen, and under US law, American citizens cannot be tried by military tribunals, White House spokesman Jay Carney said. He said since the Sept 11 attacks, the federal court system has been used to convict and incarcerate hundreds of terrorists.
Tsarnaev was charged with using and conspiring to use a weapon of mass destruction against persons and property, resulting in death.
He is also likely to face state charges in connection with the shooting death of a Massachusetts Institute of Technology police officer.
Seven days after the bombings, Boston was bustling yesterday, with runners hitting the pavement, children walking to school, and enough cars clogging the streets to make the morning commute feel almost back to normal.
Massachusetts governor Deval Patrick asked residents to observe a moment of silence at 2.50pm yesterday, the time the first of the two bombs exploded near the finish line.
Meanwhile, hundreds of family and friends packed a church in Medford yesterday for the funeral of bombing victim Krystle Campbell, 29, a restaurant worker.
A memorial service was also scheduled for last night at Boston University for Lu Lingzi, a 23-year-old graduate student from China.
Some 51 victims remained hospitalised last night, three in a critical condition.
At Snowden International School on Newbury St, a school near the bombing site, jittery parents dropped off children as teachers — some of whom had run in the race — greeted each other with hugs.
Carlotta Martin of Boston said that leaving her children at school has been the hardest part of getting back to normal.
“We’re right in the middle of things,” she said outside the school as her children, 17-year-old twins and a 15-year-old, walked in, glancing at police barricades a few yards from the school’s front door.
“I’m nervous. Hopefully, this stuff is over. I told my daughter to text me so I know everything’s OK.”
The city was also beginning to reopen sections of the six-block area around the bombing site.
Some Republican lawmakers had called for declaring Tsarnaevr an “enemy combatant”, which would give him the same status as Guantanamo “war on terror” detainees.
Republican Greg Ball had taken heat for his Twitter posting. He asked who wouldn’t want to use torture against the second suspect in the Boston bombing.
He continued to push the position in a tweet and a press release. He said he is not shy to join those who believe torture is justified in the war on terror to save lives.
Mr Ball said the Boston incident shows this may be a new normal and Americans should see it as a wake-up call to use a different set of rules.