Ramon Castillo, 36, was found hanging from a beam on the second floor of the house, wearing jeans, a gray jacket, a cap, shoes and a backpack, Gen. Javier Avalos, the regional police chief, told reporters.
Chile's most-wanted man had placed four bricks in the backpack, the prosecutor in charge of the case, Miguel Astete, told The Associated Press.
The body was identified through fingerprints that Chile sent via Interpol. Astete said officials found two bus tickets for the Urubamba Valley in his pockets and were investigating whether he might have been traveling with someone else.
Police in neighboring Chile had been seeking Castillo and other members of the sect that he led for their alleged participation in the baby's slaying on a hill in the town of Colliguay near the Chilean port of Valparaiso on Nov. 23.
The child's mother was arrested last week along with three other members of the sect. She allegedly approved the sacrifice.
Chilean police have said the baby was thrown onto a bonfire because Castillo and his followers believed the child was the antichrist.
Authorities said the 12-member sect was formed in 2005 and counted among its members professionals with university degrees.
Police said the group's rituals included using ayahuasca, a hallucinogenic plant that grows in Amazon forests.