The dust was smuggled out of Nasa by a staff photographer who gathered it from a camera the astronauts used on the lunar surface, officials said.
Nasa investigators discovered the dust - affixed to a scrap of tape - at a St Louis auction house this month.
It is illegal in the US to possess moon rocks or moon dust.
"It wasn't much to look at, but I will never be that close to the moon again," US attorney for eastern Missouri Richard Callahan said in a statement.
According to the auction material distributed by the US justice department, Nasa photographer Terry Slezak was in 1969 tasked with processing film from a camera used by Apollo 11 astronauts Buzz Aldrin and Neil Armstrong.
As he opened one of the film magazines, he found his hands covered in moon dust - apparently the camera had been dropped to the lunar surface.
That incident made Mr Slezak the first person ever to touch moon dust with his bare hands, Mr Slezak said.
He cleaned the dust from the darkroom and the film using towels and tape, and then saved a scrap of the tape, he told the New York times.
Later, he affixed the scrap of tape to a poster presented to him that was signed by the Apollo 11 astronauts.
He sold that at an auction in Germany in 2001, and told the New York Times he had never been questioned by Nasa or other officials.
Federal law enforcement officials learned this month Regency-Superior Auctions in St Louis in the state of Missouri was to list the dust.
Nasa investigators contacted the auction house, which agreed to remove it from the sale, the US justice department said in a statement.
The owner, who was not involved in the purchase and was unaware of how her late husband acquired the dust, agree to give it back to Nasa.
"Upon learning that the material had been stolen from NASA years earlier, she immediately and graciously agreed to relinquish it back to the American people," the US attorney's office said.
The US has recovered a scattering of moon dust stolen from Nasa after the 1969 Apollo 11 mission, just as it was about to be sold at auction.