As the verdict was delivered, Seale turned to his wife, Jean, and whispered, "Are you OK?"
He could receive a maximum life term for each kidnapping count.
Relatives of Dee and Moore hugged each other and cried.
'Rejoicing for justice'
Thomas Moore, Charles' elder brother who worked for years to bring the case to court, said: "I'm rejoicing for justice in this country. I see them [Dee and Moore] as rejoicing in heaven right now."
In a statement released on Thursday, Alberto Gonzales, the US attorney general, said: "Today's conviction of James Ford Seale brings some long overdue justice to the families of Henry Dee and Charles Moore, who were brutally murdered more than 40 years ago."
The main prosecution witness, another former member of the Ku Klux Klan who was granted immunity, testified during the trial that Seale told him he had killed Dee and Moore.
|A memorial in Bude, Mississippi, honours|
Charles Moore and Henry Hezekiah Dee [EPA]
The trial was the latest brought by federal prosecutors in an attempt to clear up crimes during the 1950s and 1960s by white supremacists who aimed to terrify the black community into not supporting a campaign for civil and voting rights for African-Americans in the United States' racially segregated South.
In many cases, the Ku Klux Klan and other groups were able to operate with impunity because they were supported by local law enforcement and judicial authorities.
Black Americans had few legal protections, and crimes against them often attracted little publicity.
The bodies of Dee and Moore were only recovered during a high-profile search for three civil rights activists later that year whose deaths generated widespread revulsion at the racial violence in Mississippi.
In 2005, a Mississippi jury convicted Edgar Ray Killen, a KKK member, of three counts of manslaughter in those murders, which formed the basis of the 1988 film "Mississippi Burning."