Jacob Wetterling vanished in October 1989 while playing with his brother and a friend near to his home in central Minnesota.
His remains were found and officially identified by dental records on Saturday.
Danny Heinrich, 53, admitted he kidnapped, sexually assaulted and fatally shot the boy, authorities said on Tuesday.
US attorney for the District of Minnesota Andrew Luger said Heinrich "is the confessed murderer of Jacob Wetterling, and nearly 27 years after he committed this heinous crime, he has been brought to justice. And Jacob is finally home."
Heinrich's confession, in addition to helping lead police to the spot where he buried Wetterling's body, was part of a plea deal.
He admitted federal child pornography charge but will not face charges in the killing.
Heinrich, who has been in custody since his arrest last year, also confessed to sexually assaulting another 12-year-old boy.
He faces a recommended 20-year sentence for the pornography charge, according to the US Attorney's office.
Sentencing is set for November 21.
Jacob's parents Patricia and Jerry Wetterling became tireless advocates for missing children after his disappearance.
Speaking at a press conference, Patricia, known as Patty, said: "His legacy will go on.
"For us, Jacob was alive until we found him ... we need to heal."