Okee Wade was released for three weeks in order to attend his son's funeral.
Police say the toddler was tortured for weeks by the Kryzie King, who was supposed to be taking care of him after Wade was arrested.
King is charged with assault after allegedly telling investigators she had starved Dobson for several days and also bound, beaten and burned him.
Wade turned himself in one hour after the deadline Thursday and has agreed to serve five years in prison for bank fraud.
He had full custody of his son before he was arrested, and he's been given a three-week furlough from jail to attend Myls' funeral.
"The first tragedy is me being locked up, and I couldn't get my son," Wade said. "And I begged them to at least let me get my son, but they said they wasn't going to let me out. Then the other tragedy is my son is murdered."
The boy's body was released to his mother, even though she did not have custody at the time of his death.
Dobson was laid to rest on January 21 in front of mourners who gathered at First Corinthian Baptist Church in Harlem, with the Reverend Al Sharpton delivering the eulogy.