Former Generals Carlos Eugenio Vides Casanova and Jose Guillermo Garcia, who live in the US, were sued by three victims tortured during El Salvador's prolonged civil war.
They have been now been ordered to pay $54.6m in reparations to the three - a church worker, a doctor and a professor - who later fled their country.
Defence lawyer Kurt Klaus said he would advise the generals to appeal because they are unable to pay the sum.
Two of the victims, Carlos Mauricio and Neris Gonzalez, who were in court, wept as the verdict was read.
Question of knowledge
The 10-member jury in Florida deliberated for 20 hours before reaching their decision.
They had been asked to determine whether the generals knew that their troops were torturing and murdering civilians but did not prevent it.
"This reign of terror involved tens of thousands of deaths and torture.
"You have a historic opportunity and a historic obligation to set the record straight and to tell these generals what they did was wrong," lawyer James Green said in his closing argument.
The torture victims included a doctor, Juan Romagoza Arce, who was beaten, raped and shot while being interrogated over 22 days.
Raped whilst pregnant
Mr Romagoza's fingers were damaged beyond repair after being bound by wire cables.
He said on one occasion during his ordeal Vides visited him when he was chained to the floor.
Church worker Ms Gonzalez was eight months pregnant when she was abducted.
She was beaten and raped repeatedly before being put on a truck filled with dead bodies and released.
Her baby son was born but died two months later from injuries sustained.
Mr Mauricio was suspended from the ceiling by his hands, starved and beaten during his eight day of torture.
Speaking to the BBC afterwards Mr Mauricio said he was delighted by the verdict.
"My feelings are overwhelming - I am happy, I am proud, I feel so good right now... This has been a long, long struggle for justice," he said.
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