Police found the body of the boy at the Riverwood unit about 4pm on Wednesday after responding to a "concern for welfare" call.
Mr Vikatos, who was also in the apartment with critical self-inflicted injuries, was treated at the scene.
He remained under police guard in hospital on Thursday in a stable condition after surgery.
Superintendent Sheridan Waldau said the apartment complex had been declared a crime scene.
"The Homicide Squad has been contacted and they are now on the scene and assisting us with those inquiries," she said on Wednesday.
The attack on the child appeared to be a "horrific" domestic violence-related incident, she said.
Police believe the mother of the boy died a few years ago and the child was living with Mr Vikatos and one of his female relatives, who called police.
Mr Vikatos has a partner who is also helping police.
"Any kind of incident involving a small child is always a tragic incident and our condolences go out to the family of the child," Supt Waldau said.
"We attend 140,000 (domestic violence) incidents every year and unfortunately some of them end up in homicides."
Prevention of Domestic Violence Minister Jodie Harrison said the child's death was "shocking and tragic".
She offered her condolences to the family and friends.
"This week has seen two horrendous examples of families impacted by domestic violence," she told parliament during Question Time.
The latest tragedy follows the death of 34-year-old Tatiana Dokhotaru, whose body was found in a western Sydney apartment on Saturday.
Danny Zayak, 28, has been charged with 18 domestic violence-related offences and a bail review is scheduled for Friday.
"The impact on the families and community is nothing short of devastating," Ms Harrison said.
The responsibility to end gender inequality and gender-based violence was one borne by every citizen, she said.
"As long as tolerance of any form of violence against women and children continues in our community, the battle to overcome the daily scourge of domestic and family violence will be an uphill one," she said.
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