Patricia Smith and Charles Woods, parents of Sean Smith and Tyrone Woods, filed a lawsuit against Mrs Clinton for wrongful death and defamation.
The suit claims the former secretary of state's use of a private email server contributed to their sons' death.
The parents also accuse her of defaming them in statements to the media.
Islamic militants attacked a US diplomatic compound in 2012 and killed four Americans, including ambassador Chris Stevens, while Mrs Clinton was secretary of state.
Though a House Republicans committee cleared Mrs Clinton of any wrongdoing earlier this year, the issue has dogged her presidential campaign.
The suit was filed on behalf of the parents by the conservative group Freedom Watch.
Those details, the suit argued, could have been obtained by "hostile adversaries" who may have hacked her server and ultimately led to their sons's deaths.
FBI director James Comey announced last month that it was "possible that hostile actors gained access" to Mrs Clinton's email server, but added the agency did not find conclusive evidence that it was hacked.
Chris Stevens, the sister of ambassador Stevens, told The New Yorker earlier this year that she did not blame Mrs Clinton, saying it was "inappropriate" to make the Benghazi attacks as a political issue.
"The Benghazi Mission was understaffed. We know that now. But, again, Chris knew that," she said. "It is not something they did to him. It is something he took on himself."
The suit also claims Mrs Clinton made "false and defamatory statements negligently, recklessly and purposefully and/or intentionally with malice" in public statements.
The parents said Mrs Clinton blamed the attack on a controversial YouTube video mocking the Islamic prophet Muhammad, but later denied making those statements.
Nick Merrill, a Clinton campaign spokesman, said in response to the suit: "While no one can imagine the pain of the families of the brave Americans we lost at Benghazi, there have been nine different investigations into this attack and none found any evidence whatsoever of any wrongdoing on the part of Hillary Clinton."