Lionel Tate, who was 12 when he beat 6-year-old Tiffany Eunick to death almost five years ago, declined to speak but offered through his attorney to meet with the girl's mother.
Before the plea, the mother told the court that Tate committed a "brutal murder," but said she forgave him. Tate, wearing a tan suit and an open collar, showed little reaction as he listened to her.
"This was not child's play. This was not roughhousing. This was a brutal murder," Deweese Eunick-Paul said.
"I firmly believe in God and I believe in forgiveness. I so much believe in God and for that I have forgiven you, Lionel," she said.
Eunick-Paul also said she wanted Tate, 16, to publicly acknowledge that her daughter's death was not an accident.
And she also blasted Tate's mother for not doing more to help her dying daugher. In documents obtained by CBS News, Kathleen Grosset-Tate testified her only response was to yell down the stairs - "Tiffany stop making that noise, or I'm going to spank your butt."
Grosset-Tate was also investigated - but ultimately never charged - for allegedly trying to help her son get away with murder, reports CBS News Correspondent Mark Strassmann.
His attorney, Richard Rosenbaum, said Tate was remorseful for Tiffany's death and had looked at her photograph earlier Thursday.
"By entering the guilty plea, Lionel has accepted the responsibility for Tiffany's death," Rosenbaum said.
An appeals court threw out Tate's first-degree murder conviction last month, ruling he might not have understood the criminal proceedings against him four years ago.
Instead of holding another trial, prosecutors offered Tate a plea that would sentence him to the three years he has already served. He was released earlier this week and had to enter the plea to finalize the deal.
Tate had claimed he accidentally killed the girl while imitating professional wrestling moves he had seen on television. Tate, who turns 17 on Friday, now says he leaped from a staircase and accidentally landed on her chest.
Tiffany suffered a fractured skull, lacerated liver and at least 35 other injuries.
As part of the deal, Tate will be under house arrest for a year and probation for 10 years. He also must complete 1,000 hours of community service and receive regular counseling.
Circuit Judge Joel Lazarus said he was convinced that Tate understood that one violation of the agreement would send him back to prison.
"I'm sure you feel a great weight was lifted from your shoulders ... but a new and different weight has been placed upon you," Lazarus said. "For the first time in 3 years, you will have the opportunity to make your own decisions."
Tate's plea follows several years of contentious debate over a Florida law that requires children convicted of first-degree murder to get life in prison without parole.
One Florida lawmaker has filed legislation that would allow children under 16 the eligibility of parole if they had not been previously convicted of violent crimes.