Two-year-old Sebastian Rios was found safe and his father, 27-year-old Tyler Rios of Highland Park, was taken into custody, CBS2's Christina Fan reported.
The boy's mother, 24-year-old Yasemin Uyar, is still missing.
Rios allegedly abducted the boy and his mother Friday.
Police identified Rios as a suspect after Sebastian did not show up for day care and Uyar did not arrive for her scheduled shift at work.
Officers conducted a wellness check at Uyar's home on Westfield Avenue in Rahway, where neighbors told CBS2 she and Sebastian live.
AMBER Alert notifications were sent around 2:40 p.m. Friday after police did not find anyone at the home.
Rios remains in custody in Tennessee and is awaiting extradition back to New Jersey, where he will face criminal charges.
Friends and family of Uyar gathered at the Reformed Church on Highland Park on Saturday to pray for the safe return of the young mother.
Inside, it was an incredibly emotional scene as Karen Uyar waits desperately for answers about her daughter.
"I mean, we're just overjoyed that Sebastian is back, but our focus, as much as it's on Sebastian, is also on finding Yasemin," Karen Uyar told CBS2's Nick Caloway.
Yasemin's car may also be unaccounted for. It's a 2018 silver Ford Fiesta with New Jersey plates W421713.
"If we can find her car, then we have a big lead in finding her," Karen Uyar said.
"Pretty much just hoping that she's safe for the sake of her, her family and everybody else. It's hit a lot of people," said Robyn Morris, a friend of Yasemin's.
Family and friends say Sebastian's father has a history of abusing Yasemin. They say she had a restraining order against him.
"Typical textbook case of domestic violence. Progressively got worse and this is where it's ending," Morris said.
Still, this alleged abduction was shocking for Yasemin's mother, who is pleading for help and not giving up hope.
"Still holding onto hope. I'm still holding onto hope. We're praying. Sebastian needs his mom, and we just want her back home," she said.
Anyone with information on Uyar's whereabouts is urged to call the Union County Prosecutor's Office.
CBS2's Christina Fan and Nick Caloway contributed to this report.
for more features.