Auctioneer Joe Dunning introduced the lot as "an exceptionally rare artifact from mankind's greatest achievement." It sold to an anonymous buyer on the telephone following a sluggish five-minute bidding war.
Its previous owner was an Illinois lawyer, who bought it in 2015 for $995.
But even with the buyer's premium added to Thursday's $1.5-million hammer price, the bag fell short of Sotheby's pre-sale estimate of $2-4 million.
Sotheby's said it was the only artifact from the Apollo 11 mission left in private hands. After Apollo 11 returned to Earth, nearly all the equipment from the mission was sent to the Smithsonian, the world's largest museum.
But an inventory error left the sample bag languishing in a box at the Johnson Space Center.
Staff were about to throw it out before offering it to a collector who ran a space museum in Kansas, keeping it unaware of its provenance.
When the collector was later convicted of theft, fraud and money laundering, the FBI seized the box from his garage to auction it off for restitution.
The bag -- which has a tear and is made of the same fire-retardant material as space suits -- was offered four times for sale, before the Illinois lawyer bought it in 2015.
Noticing dark smudges inside, she sent it to NASA for testing, which confirmed in 2016 it was indeed moon dust from the Apollo 11 landing site, and that it was the decontamination bag listed in the Apollo 11 stowage list.