Judge Victor Montiglio's arrest order in connection with Operation Colombo came one day after another magistrate placed Pinochet under house arrest in a fraud case.
Judge Montiglio's decision to prosecute Pinochet over Operation Colombo comes six days after he questioned the ex-dictator along with the former head of the DINA secret police, retired general Manuel Contreras.
He interrogated both to determine who ordered the operation, in which 119 members of the Revolutionary Leftist Movement (MIR) disappeared while in custody in July 1975.
Judge Montiglio charged General Pinochet in the disappearance of at least three of those dissidents.
During his recent questioning, General Pinochet was quoted in official records as saying: "I regret and suffer for these (human) losses, but God will forgive me if I have committed excesses, ... which I do not believe."
About 3,000 people are believed to have been killed during the junta years from 1973-1990, but many more were imprisoned and tortured.
On Wednesday, Judge Carlos Cerda ordered that Pinochet be placed under house arrest on charges of fraud, providing falsified documents and making false declarations to avoid paying taxes.
Judge Cerda had questioned General Pinochet on the origin of about 27 million dollars in bank accounts in the United States and a number of tax havens.
A US Senate investigation announced in June 2004 that General Pinochet had stashed millions of dollars at the US bank Riggs and banks in other countries.
But shortly after his house arrest order on Wednesday, Judge Cerda said that General Pinochet, who turns 90 on Friday, could post bail, saying he did not pose a threat to society.
An appeals court on Thursday upheld General Pinochet's provisional release in the fraud case but cut the bail by half, from 22,600 dollars to 11,300 dollars.
The former dictator has yet to post bail in the fraud case.
The Supreme Court withdrew General Pinochet's immunity from prosecution as a former head of state so he could stand trial for the bank accounts and Operation Colombo.
Doctors have declared that General Pinochet is fit to stand trial.