He was convicted and sentenced in 2005, along with several of his subordinates, in the killing of 12 suspected members of the Manuel Rodriguez Patriotic Front in June 1987.
Local media say Operation Albania was an act of vengeance by CNI agents after members of the guerrilla group allegedly tried to assassinate General Augusto Pinochet in September 1986.
The government initially said the suspected guerrillas had been killed in clashes with security agents, but a judicial investigation revealed they were killed in three separate incidents after being arrested.
On Tuesday, Salas Wendzel's attorney, Juan Carlos Manns, and officials at the Supreme Court confirmed the ruling, which cannot be appealed.
Salas Wendzel is free on bail.
The court also increased a sentence to 20 years in prison from 15 years against retired Major Alvaro Corvalan Castilla, who headed the operation that led to the killings.
Pinochet died of heart failure at the age of 91 in December without being brought to trial after his defence lawyers argued he was too ill to face charges.