Oquan Blake, 24, of Newark was arrested without incident at his mother's house late Thursday night.
He's accused of raping and murdering Dalaysia Rhymer, the daughter of a woman he had been dating. He is not the child's father.
Authorities said Blake flew into a rage when the baby's mother spent time with a friend.
The mother left her daughter in Blake's care on June 26. When the baby's grandmother unexpectedly had to go to a hospital with back pain, Blake was alone with the baby.
Before long, authorities said he called the child's mother, saying the baby was getting on his nerves and asking her to come home.
Officials said the baby's mother had planned to attend a gay pride rally in Manhattan, which irritated him, but he grew even angrier when he learned the baby's mother had skipped the event and was instead at a friend's house.
She returned home to find the baby unresponsive and took her to a hospital, where she died two days later.
Dalaysia Rhymer had a fractured skull, a ruptured spleen, broken ribs, bruising to the spine and a lacerated liver. It was also determined that the baby was sexually assaulted.
Blake and the child's mother, whose identity was not released, had been dating for about three months. He had previously cared for the infant but never by himself.
Bail has been set at $2 million.
The baby's biological father lives out of state.