The ashes were owned by Johnny Carson's ex-wife Joanne, who was one of Capote's closest friends and who died last year.
Capote, whose seminal books included In Cold Blood and Breakfast At Tiffany's, died in Carson's home in 1984.
After his death, Joanne received a portion of his ashes, which have been valued up to $6,000 (Â£4,500).
"[Joanne] often said the ashes brought her great comfort," according to Julien's Auctions, who will offer the macabre memorabilia for sale on 24 September.
Capote was a frequent guest on Johnny Carson's Tonight show, which led him to become "best buddies" with Joanne Carson, as she later described it.
He often lived and wrote at Carson's Los Angeles home until his death. Joanne told Vanity Fair in 2012: "He had a writing room in my house - he spent a lot of time here because it was a safe place and nobody could get to him."
Fans of writer Truman Capote will have the chance to get their hands on an unusual and particularly macabre piece of memorabilia - his ashes.