Officers went to General Pinochet's home in the elegant La Dehesa neighborhood of the Chilean capital Santiago where has been under house arrest for five weeks.
General Pinochet was fingerprinted and photographed with police taking both a head shot and profile.
Judge Victor Montiglio, who ordered the procedure, granted a A$63,000 bail to the former strongman. The bail must be ratified by a court of appeals.
It was the first time ever that the former Chilean president has been officially booked.
This is despite facing prosecution three times in the last five years on charges relating to the deaths or disappearances of about 3,000 people during his 1973-1990 regime.
Insult
"There is no doubt, it's an insult," said Pinochet lawyer Pablo Rodriguez after Judge Montiglio ordered the procedure.
General Pinochet, 90, who was put under house arrest on November 23 after being charged in connection with the deaths of political opponents in 1975, lost a second appeal for release on grounds of ill health Monday in Chile's Supreme Court.
Judges voted three to two against General Pinochet's habeas corpus appeal to have his house arrest lifted and the charges against him dropped.
General Pinochet is accused on involvement in the deaths of 119 political opponents in 1975 at the hands of the secret police in the notorious Operation Colombo.
He has also been charged with fraud, providing falsified documents and making false declarations to avoid paying taxes, in connection with A$37 million he allegedly hid in US and other overseas bank accounts.
The Supreme Court rejected an earlier habeas corpus appeal for General Pinochet on December 2.
In both cases, General Pinochet's attorneys argued that his mental health would prevent him from receiving a proper trial.