Chief Justice Jose Benquis said the court voted 10-6 to strip the 89-year former ruler of the immunity from prosecution he enjoys as former president, and authorize his trial in the case known as "Operation Colombo."
Pinochet is expected to be charged with the kidnapping and murder of the 15 victims, as expressed in the original request the judge filed in a lower court to strip his immunity.
The cases involved the killing of 119 dissidents, but Pinochet's case would be limited to the 15 victims whose relatives filed a criminal suit against him.
The victims' bodies were found in neighboring Argentina in 1975 and the Pinochet regime at the time said they had died in clashes among rival armed opposition groups. It supported its claim exhibiting reports in two magazines — Lea of Argentina and O Dia of Brazil. But both magazines published only that issue and then disappeared.
Wednesday's ruling, which cannot be appealed, specifically authorized the judge handling the case, Victor Montiglio, to try Pinochet. Montiglio did not immediately announce his plans.
Pinochet was not required to appear in court and remained secluded at his guarded suburban Santiago mansion. His lawyers did not immediately comment.