Twenty-four-year-old Justin Charles, of South Fork, pleaded guilty Wednesday and will be sentenced Sept. 25 by a Cambria County judge.
The judge had previously refused to throw out statements Charles made to police after county detectives seized his son's body at the funeral service.
Public defender Patricia Moore had argued Charles was so stressed by the seizure that his statements later were not made voluntarily.
Prosecutors say Charles shook Justin Jr. when he became frustrated while babysitting the child on Dec. 23, 2010. The baby died of brain injuries, but also had leg fractures that were days old by the time he died.
Moore says Charles was "stressed" but "is not an evil person."