The 30-count indictment includes many of the same weapon-of-mass-destruction 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.
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 mention of any direct overseas contacts with extremists. Instead, the indictment suggests the Internet played a central role in the suspects' radicalization.
The papers detail how, after using the Internet to study jihad propaganda and bomb-making instructions, the brothers placed knapsacks containing shrapnel-packed pressure-cooker bombs near the finish line of the 26.2-mile race.
The court papers also confirm that Dzhokhar Tsarnaev inadvertently contributed to his brother's death by running him over during a shootout with police.
The charges also cover the slaying of Massachusetts Institute of Technology police officer Sean Collier, who authorities say was shot in his cruiser by the Tsarnaevs during their getaway attempt. The brothers tried to take his gun, prosecutors said.
Tom Hays reported from New York.