Judge Alejandro Solis ordered the arrest of Pinochet for 36 cases of kidnapping, one of homicide and for 23 cases of torture at the Villa Grimaldi, a political detention centre run by Mr Pinochet's secret police where thousands of people were tortured between 1974 and 1977.
"I am not going to give any details until Monday, when he will be judicially notified," he said outside the court house.
Judge Solis, in charge of the Villa Grimaldi investigation, questioned Mr Pinochet this month about what happened at the former detention centre in the Chilean capital of Santiago.
Mr Pinochet was forced to cancel celebrations for his 90th birthday last November after he was placed under house arrest on charges related to the disappearance and presumed death of three leftists during his 17-year rule.
The house arrest, also on charges of tax fraud, lasted for seven weeks, ending in early January, when he was granted bail.
Mr Pinochet has been diagnosed with mild dementia caused by frequent mini-strokes and he has avoided trial in other human rights cases on the basis he was too ill to stand trial.
"I don't think it has been proven that he is mentally ill," said Mr Solis, who last met the former dictator on October 18, and remarked on how healthy Pinochet was looking.
During that interview, Pinochet denied responsibility for the torture of opponents at Villa Grimaldi, one of the country's most infamous secret detention centres.
He told Mr Solis he was not involved in what happened and had no knowledge of it.
Villa Grimaldi is also the prison where Chilean President Michelle Bachelet, the country's first woman president, was held and tortured three decades ago. Ms Bachelet's case is not among those Pinochet has been questioned about.
Mr Pinochet was first arrested in 1998 in London on an international warrant issued by Spanish judge Baltazar Garzon.
He was released in 2000, after 16 months of house arrest, on the grounds he was medically unfit to be tried.