Lawyers for the relatives of those who disappeared under Operation Condor, a top-secret program among South American dictatorships, argue Pinochet, 88, bears responsibility for the disappearances during his tenure.
In its ruling, the country's highest court upheld a lower court's decision clearing the way for Pinochet's prosecution. The ex general ruled here from 1973 to 1990.
The decision is a victory for lawyers who had challenged Pinochet's immunity. They claim he knew about the assassinations and disappearances that were orchestrated by Chile's secret services (DINA) under his regime.
Operation Condor was a top-secret program among dictatorships in Argentina, Bolivia, Brazil, Chile, Paraguay and Uruguay which co-ordinated repression of political opposition across South America and spirited bodies to foreign countries.
During the nearly 17 years of Pinochet's rule, some 3,000 people, by official accounting, were murdered or "disappeared" while under state custody and are presumed to have been murdered.
Pinochet has avoided trial for any of them.
The former dictator avoided prosecution for 75 murders in the "Caravan of Death," when a band of soldiers roamed Chile executing suspected opponents shortly after the 1973 coup that swept Pinochet into power.
Facing those charges, Pinochet's lawyers claimed he suffered from a mild dementia that prevented him from testifying, a position they backed up with three psychiatric reports.
However, Pinochet's subsequent appearance on a Miami television show, where he joked with the interviewer, undercut his claim.
That interview appeared to sway the lower court judges toward removing his immunity.