Vernon Henry is charged with first-degree murder in connection with the death of Adonta McCoy at the South Side residence they shared with the boy's mother in the 6900 block of South Cornell Avenue, authorities said.
Adonta was injured about 7:45 p.m. Thursday, and taken to Comer Children's Hospital where he died Saturday, according to police and the Cook County medical examiner's office.
Henry beat and choked the boy, Assistant State's Attorney Jacqueline Kwilos said at a bond hearing Sunday.
He called the boy a "crybaby" and said he needed to be toughened up, Kwilos said.
According to court documents, the mother went to visit a relative and left Henry and the boy alone in the apartment where they all lived.
When the boy started to cry, Henry lifted him off the floor by his arms and "violently shook" him, court documents allege.
The baby's head snapped forward and backward but he kept crying, and Henry put his hands around the child's throat and choked him, prosecutors claim.
At that point, the child was "gasping for air" but still sobbing, at which point Henry shoved the child face-first into a dresser, according to court documents.
When the mother came home and discovered the injuries, Henry allegedly told her they would claim the boy fell during a bath and hit his head, court documents claim.
Henry, who police initially said lived in the 6600 block of South Paulina but prosecutors later said lived with the boy and his mother, later admitted to shaking, choking and shoving the boy, prosecutors claim.
The child suffered severe brain injuries and died after two days on life support, according to prosecutors.
Authorities had previously said the boy had suffered burns, but prosecutors did not mention any burns during Sunday's hearing.
Judge Adam Bourgeois Jr. ordered Henry held without bond.
The Illinois Department of Child and Family Services is investigating the boy's mother and boyfriend for allegations of abuse, spokeswoman Veronica Resa said.
The agency has had no prior reports regarding the family, and there are no other children in the home, she said.