The declaration came just under a week before the 40th anniversary of the September 11 coup that brought the general to power, and days after a national judges' association issued an apology to those who sought missing loved ones only to have courts shrug them off.
"We have come to the conviction that there is not other attitude than explicit recognition of the serious acts and omissions that occurred at the time," said Ruben Ballesteros, president of the nation's top court, in a statement after a meeting of the full panel.
Chilean courts rejected about 5,000 cases seeking help on locating missing loved ones abducted or killed by the regime, saying they had no information about their fate.
Authorities believe the Cold War-era Pinochet regime was responsible for at least 3,200 killings and 38,000 cases of torture.
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However, the court's declaration fell short of asking for forgiveness from victims and their families.
A former president of the court, Milton Juica, who participated in the meeting today, told reporters that an eventual apology was considered, but it was decided it should be done in a more "personal" form.