Shamsid-Din Abdur-Raheem sat silently as his attorney entered the plea in state Superior Court in New Brunswick.
The 22-year-old Galloway Township resident is charged with murder and five other counts related to the infant's abduction and death. He remains jailed on $2.7 million bail.
Abdur-Raheem is also charged with attempted murder for allegedly assaulting the baby's maternal grandmother, who was baby-sitting while the child's mother sought a restraining order against him.
Prosecutors claim Abdur-Raheem abducted Zara Malani-lin Abdur from her grandmother's East Orange apartment on Feb. 16, choking and assaulting the woman and then hitting her with his van as she attempted to block his escape.
Abdur-Raheem later parked on the shoulder of the Garden State Parkway over the Driscoll Bridge - which spans the Raritan River between Sayreville and Woodbridge - and threw or dropped the baby from the front passenger window, according to court papers.
Police launched a massive search for the child. But she wasn't found until April, when people walking along the riverbank not far from the bridge came across an infant's body matching her description. An autopsy determined she had drowned.
Deputy Attorney General Andrew C. Fried asked state Superior Court Judge Frederick DeVesa Tuesday to bar Abdur-Raheem from all further contact with the baby's mother, saying he had sent her a 10-page letter from jail. Fried declined to discuss the letter's content, but said it could prompt the state to pursue additional charges of harassment or witness tampering.
Abdur-Raheem's attorney, Richard Klein, told the judge that the letter had been sent in response to a jail visit the baby's mother had initiated. Fried countered that the mother had only visited to ask Abdur-Raheem if their child was still alive, before the baby's body had been found.
The judge asked Abdur-Raheem if he understood the order to have no further contact with the child's mother, to which the defendant, his cuffed hands resting in his lap, nodded and quietly replied: "Yes."
The case, which New Jersey Attorney General Paula Dow has characterized as a tragic example of domestic violence, prompted a review of the state's guidelines for issuing Amber Alert broadcasts in response to reports of missing children.
Dow ordered the review, and changes to the system, after it was discovered that no alert had been issued for four hours between the time the child was abducted and Abdur-Raheem was arrested, as state law discouraged the use of the alerts in domestic cases at the time.
New Jersey police now issue the alerts even in cases of suspected parental involvement in a child's abduction.