Nathalyz Rivera died at a hospital shortly before 2 a.m. EDT, Philly.com reported.
"This is one of the worst cases of abuse that I've seen in my five years at the homicide unit," Capt. James Clark told reporters. "I saw the photos and even for me, they were difficult to look at."
The girl was one of five children living with their 30-year-old father, Carlos Rivera, who hadn't been seen since dropping off the other children at a relative's home, the news website said.
Investigators were talking to the girl's mother, who was staying with a male friend, Clark said.
Clark said the medical examiner's autopsy determined Nathalyz's death was homicide by starvation. The captain said the girl, who was a twin, had serious disabilities and had not been to a doctor in more than a year. She also had bruises, he said, "but that might have been from fleas or mice."
The home where the children lived was in "bad shape," Clark said.