The jury voted 6-1 to acquit 75-year-old Valentina Andrade, who was accused of planning and ordering the mutilations and killings as part of a black magic ritual, a court official said by telephone from Belem, 2,400 kilometers (1,500 miles) northwest of Rio de Janeiro.
Andrade was charged in the killing of three boys and the castration of two more.
Four other defendants were convicted in earlier trials in connection with the killings and mutilations which occurred in the western Amazon city of Altamira, between 1989 and 1992. They are serving sentences ranging from 30 to 70 years in prison.
At least 14 boys, ranging in age from 12 to 17, were believed to have been abducted over a period of four years. Six were found dead, with their sexual organs missing. Three more were mutilated but survived and five more are still missing.
The defendants, who authorities said were members of an alleged satanic group known as the Superior Universal Alignment sect, were charged in three murders and two mutilations.
The gruesome killings shocked Brazil when they were first reported and sparked fear in the farming community in the heart of the Amazon rainforest.