Tsarnaev, 19, was charged in his hospital room, where he was in serious condition with a gunshot wound to the throat and other injuries suffered during his attempted getaway. His older brother, Tamerlan, 26, died Friday after a fierce gunbattle with police.
The Massachusetts college student was charged with using and conspiring to use a weapon of mass destruction. He was accused of joining with his brother in setting off the shrapnel-packed pressure-cooker bombs that killed three people and wounded more than 200 a week ago.
The brothers, ethnic Chechens from Russia who had been living in the U.S. for about a decade, practiced Islam.
Two U.S. officials said preliminary evidence from the younger man's interrogation suggests the brothers were motivated by religious extremism but were apparently not involved with Islamic terrorist organizations.
Dzhokhar communicated with his interrogators in writing, precluding the type of back-and-forth exchanges often crucial to establishing key facts, said the officials, who spoke on condition of anonymity because they were not authorized to discuss the investigation publicly.
They cautioned that they were still trying to verify what they were told by Tsarnaev and were looking at such things as his telephone and online communications and his associations with others.
In the criminal complaint outlining the allegations, investigators said Tsarnaev and his brother each placed a knapsack containing a bomb in the crowd near the finish line of the 26.2-mile race.
The FBI said surveillance-camera footage showed Dzhokhar manipulating his cellphone and lifting it to his ear just instants before the two blasts.
After the first blast, a block away from Dzhokhar, "virtually every head turns to the east ... and stares in that direction in apparent bewilderment and alarm," the complaint says. Dzhokhar Tsarnaev, "virtually alone of the individuals in front of the restaurant, appears calm."
He then quickly walked away, leaving a knapsack on the ground; about 10 seconds later, a bomb blew up at the spot where he had been standing, the FBI said.
The FBI did not say whether he was using his cellphone to detonate one or both of the bombs or whether he was talking to someone.
The criminal complaint shed no light on the motive for the attack.
The Obama administration said it had no choice but to prosecute Dzhokhar Tsarnaev in the federal court system. Some politicians had suggested he be tried as an enemy combatant in front of a military tribunal, where defendants are denied some of the usual constitutional protections.
But Tsarnaev is a naturalized U.S. citizen, and under U.S. law, American citizens cannot be tried by military tribunals, White House spokesman Jay Carney said. Carney said that since 9/11, the federal court system has been used to convict and imprison hundreds of terrorists.
Also on Monday, Kazakhstan's Ministry of Foreign Affairs issued a statement saying two foreign nationals arrested Saturday in the Boston area on immigration violations are from Kazakhstan and may have known the two Marathon bombing suspects.
The foreign ministry said U.S. authorities came across them while searching for "possible links and contacts" to Dzhokhar Tsarnaev. Their names have not been released.
Shortly after the charges against Tsarnaev were unveiled, Boston-area residents and many of their well-wishers - including President Barack Obama at the White House - observed a moment of silence at 2:49 p.m. - the moment a week earlier when the bombs exploded.
Across Massachusetts, the silence was broken by the tolling of church bells.
"God bless the people of Massachusetts," said Gov. Deval Patrick at a ceremony outside the Statehouse. "Boston Strong."
Also Monday, the governor and Roman Catholic Cardinal Sean O'Malley were among the mourners at St. Joseph Church at the first funeral for one of the victims, Krystle Campbell. The 29-year-old restaurant manager had gone to watch a friend finish the race.
"She was always there for people. As long as Krystle was around, you were OK," said Marishi Charles, who attended the Mass. "These were the words her family wanted you to remember."
Amid a swirl of emotions in Boston, there was cause for some celebration: Doctors announced that everyone injured in the blasts who made it to a hospital alive now seems likely to survive.
That includes several people who arrived with legs attached by just a little skin, a 3-year-old boy with a head wound and bleeding on the brain, and a little girl riddled with nails.
"All I feel is joy," said Dr. George Velmahos, chief of trauma surgery at Massachusetts General Hospital, referring to his hospital's 31 blast patients. "Whoever came in alive stayed alive."
As of Monday, 51 people remained hospitalized, three of them in critical condition. At least 14 people lost all or part of a limb; three of them lost more than one.
Dzhokhar Tsarnaev had gunshot wounds to the head, neck, legs and hands when he was captured hiding out in a boat in a backyard in the Boston suburb of Watertown, authorities said.
A probable cause hearing - at which prosecutors will spell out the basics of their case - was set for May 30. According to a clerk's notes of Monday's proceedings in the hospital, U.S. Magistrate Judge Marianne Bowler indicated she was satisfied that Tsarnaev was "alert and able to respond to the charges."
Tsarnaev did not speak during the proceeding, except to answer "no" when he was asked if he could afford his own lawyer, according to the notes. He nodded when asked if he was able to answer some questions and whether he understood his rights as explained to him by the judge.
Federal Public Defender Miriam Conrad, whose office has been assigned to represent Tsarnaev, declined to comment.
Tsarnaev could also face state charges in the slaying of a Massachusetts Institute of Technology police officer, who was shot in his cruiser Thursday night on the MIT campus in Cambridge.
News of the criminal charges pleased some of the people gathered at a makeshift memorial along the police barricades on Boylston Street, where the attack took place.
Amy McPate a Massachusetts native now living in Maine, said she usually opposes the death penalty, but thinks it should apply in this case.
"They were more than murderers. They're terrorists. They terrorized the city," she said. "The nation has been terrorized."
Kaitlynn Cates of Everett, who suffered a leg injury in the bombing, said from her hospital room: "He has what's coming to him."
Among the details in the FBI affidavit:
- One of the brothers - it wasn't clear which one - told a carjacking victim during their getaway attempt, "Did you hear about the Boston explosion? I did that."
-The FBI said it searched Tsarnaev's dorm room at the University of Massachusetts-Dartmouth on Sunday and found BBs as well as a white hat and dark jacket that look like those worn by one of the suspected bombers in the surveillance photos the FBI released a few days after the attack.
Associated Press writers Steve Peoples, Allen Breed, Bridget Murphy, Jay Lindsay and Bob Salsberg in Boston contributed to this report.