"This case is an outstanding example of our ongoing, vigilant efforts to prosecute racially-motivated crimes to the fullest extent of the law, regardless of how many years have passed," Alberto Gonzalez, US attorney general, said.
Seale's lawyer said he will appeal against the convictions.
A former police officer, Seale was arrested in 1964 but was released after police said they lacked sufficient evidence to prosecute him.
Seale was believed dead for years until Thomas Moore, brother of Charles Moore, located him in southern Mississippi while investigating his brother's murder.
Dee and Moore, both 19, were kidnapped in 1964 while hitch-hiking in Mississippi and taken to a forest, where Seale aimed a shotgun towards the men while his companions attacked them.
The teenagers were driven to a tributary of the Mississippi river, attached to heavy weights and thrown alive into the water from a boat, prosecutors said.
|Charles Moore was one of two men killed in an |
attack by the Klansmen 43 years ago [AFP]
Their bodies were recovered during a search for three other civil rights activists later that year.
Mississippi lies at the heart of the so-called "deep South" that was long associated with hangings and other violent attacks on blacks by the KKK and other white supremacist groups.
The main prosecution witness in the case against Seale was Charles Marcus Edward, another former Klansman who was involved in the attack on Dee and Moore.
Edward, who was granted immunity from prosecution in exchange for his testimony, told the court that Seale admitted he killed the men.
Lenard Wolf, a former agent of the Federal Bureau of Investigation (FBI) said during the trial that Seale was unmoved by the investigators' belief that he was involved in the killings.
"We know you did it, you know you did it, the Lord above knows you did it," Wolf told Seale, according to the testimony.
"Yes, but I'm not going to admit it; you are going to have to prove it," Seale answered.
While Seale was not charged with murder, the indictment claimed the abductions resulted in the deaths of Dee and Moore.
"While this sentence can never repair the suffering and loss brought by these heinous acts of racial violence, it will hopefully bring some closure to the families of Henry Dee and Charlie Moore who have waited decades for justice," said Wan Kim, US assistant attorney general for the Civil Rights Division of the Department of Justice.
A string of federal prosecutions across the US has attempted to address crimes during the 1950s and 1960s by white supremacists.
The KKK waged a violent campaign against the black community and against the struggle for civil rights for African-Americans in the southern US, where racial segregation was in place.
In many cases, such groups were supported by local law enforcement and judicial authorities, while black Americans had few legal protections.