The formal arrest on Wednesday, which included a reading of charges and a signature from the former military leader, was carried out at Pinochet's ranch in Los Boldos, west of Santiago on the Pacific coast.
Pinochet, 89, has never stood trial for the disappearance and presumed murder of some 3000 political opponents who vanished during his 1973-1990 rule.
A magistrate's secretary entered Pinochet's residence with two policemen and another court secretary who acted as a witness. They left 15 minutes later.
The charges - one murder and nine kidnappings of people whose bodies were never found - are related to Operation Condor, a 1970s conspiracy of South American dictatorships to collaborate on eliminating leftist opponents.
The former leader suffered a mild stroke in mid-December and was briefly hospitalised, but was said to be recovering.
According to Juan Guzman Tapia, the judge heading the case, Pinochet authorised Operation Condor in November 1975 following a meeting of secret services from Argentina, Bolivia, Brazil, Chile, Uruguay and Paraguay in Santiago.
The same judge had put Pinochet under house arrest for six weeks in 2001 on charges relating to some 75 summary executions carried out after the 1973 coup.
But the charges were dropped in July 2002 when the Supreme Court found that Pinochet suffered from mild dementia and was unable to stand trial.
The prosecution since then has successfully argued that the former leader was in better health. His lawyers, however, are urging the trial be halted on health grounds.