Eugenio Vides Casanova, 77, has lived in Florida since 1989 and was once regarded by the US as an ally.
He was taken into custody last month under a law designed to keep those accused of abuses in other countries from seeking refuge in the US.
But he will not face charges in El Salvador due to an amnesty law.
Eugenio Vides Casanova, once El Salvador's defence minister and head of the National Guard, arrived at the country's main airport with more than 100 other deportees, reports say.
He has been linked to the killing of four US churchwomen in 1980.
He argued against his deportation on the grounds his military tactics were backed by Washington at the time.
In a separate development, the US has begun extradition proceedings of another former Salvadoran military officer living in the US.
Inocente Orlando Montano Morales is facing charges in Spain over the killing of five Jesuit priests.
At least 70,000 people died in El Salvador's civil war from 1980-1992, fought between the country's right-wing military government and leftist rebels.
The US has deported a former general during El Salvador's civil war after a court ruled he was responsible for torture and killings while in command.