Police say Nelson Haase was arrested on Saturday and had been on the run for three years after being convicted of murdering Jara in 1973 and sentenced to 25 years in prison.
Despite the arrest, Jara's family says they are not completely satisfied.
"We learned that retired Colonel Nelson Haase Mazzei, who had been a fugitive from justice since 2023, was found and imprisoned. We appreciate this news," said Jara's daughter, Amanda Jara, in a letter.
However, she added, "it is difficult to consider this justice."
Haase, 80, was convicted in 2018 and his sentence was increased in 2023, along with those of six other military officers. The crimes are considered to be among the most emblematic examples of the brutality that marked the 17-year Pinochet dictatorship.
The former official fled before beginning his prison term.
Judge Paola Plaza of the Santiago Court of Appeals ordered Haase's "immediate imprisonment," the judiciary said in a statement.
The institution added Haase was the last of those convicted to begin serving his sentence.
Jara, who became famous in the 1960s and 70s for his protest and pacifist songs and supported the ousted socialist president Salvador Allende, was subjected to torture and shot 44 times.
He was one of about 5000 people, arrested in the immediate aftermath of the coup, who were taken to a sports stadium in Santiago.
In recent decades, Chile has established a series of truth commissions to investigate and determine responsibility for the violations committed between 1973 and 1990, ranging from murders and torture to forced disappearances and the illegal adoption of children.
Official documents estimate during its 17 years, the military dictatorship left some 40,000 victims, including more than 2000 people who were executed, 1469 victims of enforced disappearance and thousands more tortured.
Since 2024, Chile has also promoted the so-called National Search Plan aimed at outlining a road map for the search of disappeared detainees.
"We hope that the police will manage to find all those who fled for crimes against humanity," Amanda Jara concluded in her letter. She now heads the VÃctor Jara Foundation.
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