Jose Ismael Torres, 26, will spend 13 years in prison; Kayla Rae Norton, 25, is to serve six years, Atlanta news outlets report.
Both wept as the sentences were handed down yesterday in Douglas County, west of Atlanta.
"Their actions were motivated by racial hatred," said Superior Court Judge William McClain.
The judge ordered the two permanently banished from Douglas County once they are released.
The two are the last of 15 people charged in the confrontation at the 8-year-old's party, which took place in Douglasville in July 2015. Only four were charged with felonies. The other two pleaded guilty and are serving shorter prison terms.
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"This is behavior that even supporters of the Confederate battle flag can agree is criminal and shouldn't be allowed," Douglas County District Attorney Brian Fortner said in a statement.
Norton was sentenced on one count of violating Georgia's street gang act and one count of making terroristic threats. Torres was sentenced on three counts of aggravated assault with a deadly weapon, one count of terroristic threats and one count of violating the street gang act.
Roof, who was sentenced to death for his crime, brandished the battle flag in several photographs that came to light after his arrest. He said it had been his intent to kill black people and start a race war.
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