The panel of five judges voted three to two against Pinochet's habeas corpus appeal to have his house arrest lifted and the charges against him dropped.
Pinochet, 90 and in frail health, ruled Chile for 17 years after leading a 1973 coup.
He is charged in connection with the deaths of 119 political opponents 30 years ago at the hands of the secret police in the notorious Operation Colombo.
He is also charged with fraud, providing falsified documents and making false declarations to avoid paying taxes, in connection with millions of dollars he allegedly hid in US and other overseas bank accounts.
Pinochet claimed his health problems, including mild dementia caused by frequent mini-strokes, made him unfit to face a criminal process.
In the past five years, Chilean courts have thrown out three human rights cases against Pinochet due to his poor health, but some doctors on a new court-ordered medical panel have said he had exaggerated his symptoms.
Pinochet has been under house arrest since late last month.
He was indicted last month for tax fraud and other crimes related to about $US27 million ($A37 million) hidden in foreign bank accounts.
The Pinochet regime is accused of covering up the Operation Colombo deaths by planting false news stories saying members of the Revolutionary Leftist Movement killed each other in an internal dispute and armed confrontation.
At least 3,000 political opponents of Pinochet's military government were killed and tens of thousands tortured or imprisoned, according to official count.