Bridges allegedly stole $800,000 worth of bitcoins, according to the government's complaint, and kept the illicit funds in a Tokyo-based Bitcoin exchange known as Mt. Gox.
Mt. Gox infamously imploded last year after it admitted it had lost track of millions of dollars' worth of bitcoins.
The DEA official, Carl Force, was "the lead undercover agent in communication" with Roberts - a role that gave him the power to extort.
Using a series of private, fictitious accounts on Silk Road, Force allegedly told Roberts he would bury evidence related to the case if Roberts paid him $250,000.
In another instance, Force allegedly used a fake account named "French Maid" to sell Roberts confidential information related to the federal investigation.
Roberts paid $100,000 for the information, according to the complaint.
"Force and Bridges abused their positions as federal agents and engaged in a scheme to defraud a variety of third-parties, the public, and the government, all for their own financial enrichment," the complaint reads.
Steve Levin, a lawyer representing Bridges, said Bridges "maintains his innocence and will answer the charges at the appropriate time."
A lawyer representing Force did not immediately respond to a request for comment.
Force was arrested Friday; his detention hearing takes place Thursday.
Bridges turned himself in Monday; his next court date is May 5, according to Levin.
In February, a federal jury convicted 30-year-old Ross Ulbricht of running Silk Road as Dread Pirate Roberts; Ulbricht's site allowed buyers and sellers of illicit drugs to contact one another anonymously.
In addition to using his position to extract financial concessions from Roberts, Force pocketed much of the bitcoin that he secured from Roberts as part of the undercover operation, the Justice Department said in its complaint.
Some of those funds were allegedly wired to a bank account in Panama, "all in an effort to launder and conceal the true source of the ill-gotten proceeds."
When Force's account on Venmo, an online payments service, was frozen due to "suspicious activity," Force allegedly forged an official subpoena and sent it to the company without his supervisor's permission.
"Force then sought to conceal evidence of his improper use of an official subpoena," the complaint alleges.
The complaint also implies Bridges may have been involved in a massive break-in at Silk Road on January 25, 2013 - one that saw "a sizeable theft of bitcoins" transferred to Mt. Gox.
Soon thereafter, the Justice Department said, large deposits from Mt. Gox made their way into a shell company belonging to Bridges known as Quantum International Investments.
Bridges and Force are being charged with money laundering, wire fraud, theft of government property and conflict of interest.
The criminal complaint was filed in San Francisco.