Both were executed by firing squad four weeks later, the military government announced at the time.
Pinochet was stripped of his immunity from prosecution in the case last July.
More than 15 of Allende's bodyguards and aides were taken from the government palace during the coup and remain unaccounted for. Allende committed suicide during the military bombardment of the palace.
There was no immediate reaction from Pinochet's lawyers, but they were expected to appeal before the supreme court as they have done on previous occasions when the former president has been indicted.
Two cases against Pinochet were closed when the courts ruled that his health was not good enough for him to stand trial.
Pinochet has been diagnosed with a mild dementia caused by several strokes, suffers from diabetes and arthritis and needs a pacemaker.
In addition to Monday's indictment, three others are pending, two in human rights cases and one for tax evasion.
On Saturday, Pinochet issued a statement taking political, but not explicitly legal, responsibility for the actions of his military government.
"Today, near the end of my days, I want to say that I harbour no rancour against anybody, that I love my fatherland above all and that I take political responsibility for everything that was done which had no other goal than making Chile greater and avoiding its disintegration," he said.
Scores of other legal actions have been filed against Pinochet by relatives of victims of his government.
During Pinochet's rule, 3,197 people were killed for political reasons, according to an independent commission report. Thousands more were illegally imprisoned, tortured and forced into exile.