Peron is wanted by a judge for questioning over the disappearance of 24-year-old Hector Aldo Fagetti Gallego and the arrest of a minor, Jorge Valentin Beron, in 1976.
Another judge wants to question her as part of a probe into the Anti-communist Alliance, a death squad blamed for killing at least 1,500 government opponents from 1973-1976.
As for her alleged involvement in the death squad, the court said there was insufficient evidence to link Peron to the crimes "however terrible they were".
"These are crimes of common law already issued and raised to crimes against humanity [by Argentine authorities] ... so it has been decided to oppose the extradition," the court said in its ruling.
Her lawyers had argued the ex-leader should not be extradited since she is a citizen of Spian, over which Argentina does not have jurisdiction.
They also cited her advanced age and poor health as reasons against the extradition.
Peron became president in 1974 following the death of her husband, populist president Juan Peron.
She has lived in exile in Spain since being forced from government.
Isabel married Juan Peron several years after the death of his second wife, the iconic Argentine first lady Eva Peron.