The Union County Prosecutor's Office said Sebastian Rios was found safe Saturday in Monterey, Tennessee.
That's also where his father, 27-year-old Tyler Rios of Highland Park, was arrested.
Sebastian's mother, 24-year-old Yasemin Uyar, is still missing.
"I'm so grateful to have my grandson back. I'm so grateful to know that he's okay, but I am just praying every second that we find Yasemin, we call her Yazzi, that we find Yasemin," Karen Uyar, Yasemin Uyar's grandmother, said.
Tyler Rios remains in custody in Tennessee pending extradition.
"While we are relieved that Sebastian Rios has been found safe and that Tyler Rios is in custody, we are still urging anyone with information about the whereabouts of Yasmine Uyar to come forward and tell us what they know, even anonymously," Union County Prosecutor Lyndsay V. Ruotolo said.
Sebastian and Yasemin were last seen in Rahway on Thursday and were believed to have been taken by Rios.
Police set up a perimeter that included a block of residences around the home where the boy lived with his mother on Westfield Avenue.
Rahway detectives entered the home on Friday evening and said it was an active scene.
Yasemin's sister tells Eyewitness News that Tyler and Yasemin are not together, and their only relation is sharing a son. She says Tyler has a history of domestic violence and recently became homeless.
Woman prays for sister, child's safety after amber alert issued
Marissa also said that Tyler recently broke into Yasemin's home, and police officers were called. Tyler had apparently convinced the officers that he had been living there.
Marissa added that Yasemin was planning to move out of Rahway for safety concerns.
"She was pretty busy packing and trying to get herself together," Marissa said.
Marissa says she just wants to know her sister and nephew are safe, and had a message for Tyler Rios.
"Man I just want him to let at least my nephew go. I mean I want my sister to come home, but, I mean, something's got to give, you know?" she said.
Marissa is holding a search party for her sister on Saturday night.
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