The Church has long been accused of complicity with the former military dictatorship's crackdown on socialism which, according to official estimates, resulted in the deaths or disappearances of around 13,000 people.
In a joint statement on opening files at the Vatican's embassy in Buenos Aires and the Argentine bishops' conference, the two organisations said the decision was taken "in the service of truth, justice and peace".
Pope Francis, who was a Jesuit superior in Argentina during the country's dictatorship between 1976 and 1983, previously vowed to open the archives when he was challenged by family members of the disappeared or "desaparecidos".
Despite being credited with saving several people during the "dirty war", the pontiff has himself been criticised for not commenting on the atrocities publicly.
The Vatican and national Catholic Church in Argentina say work to catalogue and digitalise archives has been completed and information will be provided to allow victims access to the data.