Dias Kadyrbayev, 19, and Azamat Tazhayakov, 19, both of New Bedford were charged in a criminal complaint with conspiracy to obstruct justice by conspiring to destroy, conceal and cover up tangible objects belonging to Tsarnaev.
Prosecutors say the pair realized he was the bomber, and then disposed of a laptop computer and a backpack containing fireworks.
The FBI reportedly found the bag in a dump in New Bedford.
The third man, 19-year-old Robel Phillipos, 19, of Cambridge, was charged with willfully making materially false statements to federal law enforcement officials during a terrorism investigation.
Convictions could mean 5 to 8 years in prison.
Just hours before the police shootout, authorities say Kadyrbayev exchanged a series of text messages with Dzhokhar after seeing what looked like a familiar face being flashed on television.
"Tsarnaev's return texts contained 'lol' and other things Kadyrbayev interpreted as jokes such as 'you better not text me' and 'come to my room and take whatever you want,'" an FBI agent wrote in an affidavit.
Tazhayakov told authorities that during a meal about a month before the terror attacks, Tsarnaev informed him and Kadyrbayev "that he knew how to make a bomb."
The lawyers for the Kazakh students said their clients had nothing to do with the bombing and were just as shocked by the crime as everyone else. Phillipos' attorney, Derege Demissie, said outside court: "The only allegation is he made a misrepresentation."
Kadyrbayev and Tazhayakov have been in jail for more than a week on allegations they were in violation of their student visas, one because he was skipping classes, the other because he was no longer enrolled.
Tazhayakov was allowed to return to the U.S. from Kazakhstan in January despite not having a valid student visa, a federal law enforcement official told The Associated Press. His student visa status had been terminated because he was academically dismissed from the university, said the official, who was not authorized to discuss the case and spoke on condition of anonymity.
All three men charged Wednesday began attending UMass with Tsarnaev in 2011, according to the FBI.
Kadyrbayev, an engineering major, said he and Tazhayakov hung out with Tsarnaev on and off campus. The three often spoke Russian among themselves.
He told authorities he became "better friends" with Tsarnaev, an ethnic Chechen, in spring 2012, and that he was a frequent visitor to the Tsarnaev home in Cambridge.
It was unclear from the court papers whether authorities believe that was an instruction from Tsarnaev to destroy evidence, but the FBI said that Kadyrbayev knew when he saw the fireworks that Tsarnaev was involved in the bombings and decided to remove the backpack "to help his friend Tsarnaev avoid trouble."
Kadyrbayev also decided to remove Tsarnaev's laptop "because he did not want Tsarnaev's roommate to think he was stealing or behaving suspiciously by just taking the backpack," the FBI said.
After the three returned to Kadyrbayev's and Tazhayakov's apartment with the backpack and computer, they watched news reports featuring photographs of Tsarnaev. The FBI said Kadyrbayev told authorities the three men then "collectively decided to throw the backpack and fireworks into the trash because they did not want Tsarnaev to get into trouble."