They had not met each other since troops raided their Cancap village 30 years ago in search of leftist guerrillas. They were reunited Friday.
Mario Polanco of the Mutual Support Group (GAM), an organisation representing conflict victims, told reporters that he first met Juana Chamay at a church in southern Escuintla province and later met her sister Magdalena in the San Juan Cotzal town of northwestern Quiche region.
Troops dragged the girls' parents, Miguel Chamay and Petronila Toma, from their home, tied them up and beat them while demanding information about the rebels.
Though they eventually realised Miguel and Petronilla didn't know anything, soldiers forcibly split the family, GAM said.
Juana, who was injured during the troops' raid, was sent to a hospital in Escuintla, where she was adopted by nurse Guadalupe Mendez, who subsequently took the girl to live in Guatemala City.
"She raised me as her daughter and she gave me schooling. I reached the second year of high school and as I no longer wanted to study because I didn't like it, she found me work with Social Security (state-run healthcare) in the capital," said Juana, who is now the mother of a seven-year-old girl.
"I spent 14 years there in various jobs," she added. "I feel happy to have found my sister," Juana said Friday, adding that she had only a vague memory of their parents. "I was very little. I know that they're dead now."
Magdalena remained with her grandmother Teresa Toma in San Juan Cotzal in Quiche. She said she has two children, aged seven and nine.
A joint GAM-Red Cross programme has helped to arrange ove 100 reunions of separated relatives since 2001, Polanco said.
Guatemala's civil war left some 250,000 dead, majority of them Indian peasants, and Quiche was the province that suffered most under the army's scorched-earth policies.