The Benghazi diplomatic compound attack killed four Americans, including Ambassador Chris Stevens, while Mrs Clinton was secretary of state. The issue dogged her presidential campaign last year.
Patricia Smith and Charles Woods, parents of two of those killed, filed a lawsuit against Mrs Clinton for wrongful death and defamation.
The suit claimed the former secretary of state’s use of a private email server contributed to their sons’ deaths by exposing their details to the attackers.
The parents also accused her of defaming them in statements to the media.
But federal judge Amy Berman Jackson ruled that Mrs Clinton was acting in her official capacity while using her private email server, so the US government should be the defendant.
She also ruled that the parents should have raised, as legally required, their claims with the state department before launching their legal action. Because of this, she decided in favour of the government’s motion to dismiss the counts against it.
She judged that the parents did not have enough evidence to substantiate their claim that Mrs Clinton had called them, or implied, that they were liars.