Officers were called to a home on 87th Street just after midnight Wednesday.
There, they found 56-year-old Estrella Castaneda and her 25-year-old daughter Lina Castaneda dead in their bedrooms.
Authorities say both had serious head injuries, which appeared to have been inflicted with a hammer.
A man was taken into custody at the scene who is the mother's boyfriend.
Carlos Amarillo, 44, is charged with two counts of first-degree murder and two counts of criminal possession of a weapon.
Detectives say he waited patiently at the crime scene after calling 911 himself, claiming the women had cast a spell on him.
"Two females are dead," he told the operator. "They were assassinated. Hurry, they are dead. I killed them because they are witches. I want the police to kill me. I killed them with a hammer."
Police officers were seen moments later, carrying the younger woman's 7-year-old daughter from the house. She was not physically harmed, and it is believed she slept through the incident.
Some neighbors said they heard the hammering, but could not possibly imagine the horror unfolding inside the home.
Friends of the victims described them as quiet, private Colombian immigrants who attended the local Roman Catholic Church.