The 30-count indictment contains the bombing charges, punishable by the death penalty, that were brought against the 19-year-old Tsarnaev in April.
But prosecutors added charges covering the slaying of an MIT police officer and the carjacking of a motorist during the getaway attempt that left Tsarnaev's older brother, Tamerlan, dead.
"Tamerlan Tsarnaev's justice will be in the next world, but for his brother, accountability will begin right here in the district of Massachusetts," Suffolk District Attorney Daniel Conley, whose jurisdiction includes Boston, said at a news conference with federal prosecutors.
Three people were killed and more than 260 wounded by the two pressure-cooker bombs that went off near the finish line of the marathon on April 15.
Dzhokhar Tsarnaev was captured four days later, hiding in a boat parked in a backyard in Watertown, Mass.
According to the indictment, he scrawled messages on the inside of the vessel that said, among other things, "The U.S. Government is killing our innocent civilians," ''I can't stand to see such evil go unpunished," and "We Muslims are one body you hurt one you hurt us all."
The Tsarnaev brothers had roots in the turbulent Russian regions of Dagestan and Chechnya, which have become recruiting grounds for Islamic extremists. They had been living in the U.S. about a decade.
But the indictment made no mention of any larger conspiracy beyond the brothers, and no reference to any direct overseas contacts with extremists. Instead, the indictment suggests the Internet played an important role in the suspects' radicalization.
Before the attack, Dzhokhar Tsarnaev downloaded onto his computer the summer 2010 issue of Inspire, an online English-language magazine published by al-Qaida, according to the indictment. The issue detailed how to make bombs from pressure cookers, explosive powder extracted from fireworks, and lethal shrapnel.
He also downloaded extremist Muslim literature, including "Defense of the Muslim Lands, the First Obligation After Imam," which advocates "violence designed to terrorize the perceived enemies of Islam," the indictment said.
Another tract downloaded included a foreword by Anwar al-Awlaki, an American propagandist for al-Qaida who was killed in a U.S. drone strike, federal prosecutors said.
U.S. Attorney Carmen Ortiz of Massachusetts said it will be up to Attorney General Eric Holder to decide whether to pursue the death penalty against Tsarnaev.
The indictment assembled and confirmed details of the case that have been widely reported over the past two months, and added new pieces of information.
For example, it confirmed that Tamerlan Tsarnaev bought 48 fireworks mortar shells containing about eight pounds of explosive powder from a Seabrook, N.H., fireworks store. It also disclosed that he used the Internet to order electronic components that could be used in making bombs.
The papers detail how the brothers then placed knapsacks containing shrapnel-packed bombs near the finish line of the 26.2-mile race.
The court papers also confirm that Dzhokhar Tsarnaev contributed to his brother's death by accidentally running him over with a stolen vehicle during a shootout and police chase.
The charges cover the slaying of Massachusetts Institute of Technology police officer Sean Collier, who authorities said was shot in the head at close range in his cruiser by the Tsarnaevs during their getaway attempt. The brothers tried to take his gun, prosecutors said.
In addition, prosecutors said that during the carjacking, the Tsarnaev brothers forced the motorist to turn over his ATM card and his password, and Dzhokhar Tsarnaev withdrew $800 from the man's account.
At the same time the federal indictment was announced, Massachusetts authorities brought a 15-count state indictment against Dzhokhar Tsarnaev over the MIT officer's slaying and the police shootout.
Tom Hays reported from New York.