Judge Alejandro Madrid handed down the verdict after a 15-year investigation during which Frei's body was twice exhumed for forensic examination.
The verdict found the six defendants guilty of "homicide by poisoning after a surgical intervention," and sentenced them to between three and 10 years.
Lawyers for the Frei family described the verdict as historic.
Frei, president from 1964 to 1970, died of a sudden infection in January 1982 while he was hospitalized for hernia treatment. He was 71.
Pinochet became Chile's dictator soon after a military coup that killed Frei's successor, Salvador Allende, on September 11, 1973. Pinochet left office when democracy was restored in 1990.
Frei died when he and his Christian Democratic Party were gaining strength as the military regime's main opposition. The Pinochet regime faced its first street protests in the early 1980s.
His body was disinterred for a second time in 2016 to determine how the poison, low doses of mustard gas and thallium, had been administered.
The judge sentenced a doctor, Patricio Silva Garin, to 10 years in jail for administering the poison, causing Frei's death. Another doctor, Pedro Valdivia, was sentenced to five years as an accomplice.
Lusi Vecerra Arancibia, the ex-president's driver, and intelligence agent Raul Lillo Gutierrez were each handed seven-year sentences.
Two physicians specializing in palliative care, Helmar Rosengerg and Sergio Gonzalez, got three years for covering up the crime.
More than 3,200 people were killed under the Pinochet regime, and some 38,000 people were tortured.