The Philadelphia Medical Examiner's Office began an autopsy Monday, Health Department spokesman Jeff Moran said.
The incident is under investigation to determine whether bullying was involved and what caused O'Neill to suffer seizures and die, said Emily Harris, spokeswoman for Delaware County District Attorney Jack Whelan.
She said the investigation involves one boy, although Darby Township Police Chief Leonard McDevitt said two boys were present, one of whom allegedly punched O'Neill.
No charges have been filed in the incident, captured on video.
"It's been heartbreaking," said the boy's father, Robert, 39. "He was my best friend."
Robert O'Neill, a truck driver, said his son was a great older brother to a sister and brother. He described a smart boy who enjoyed watching sports with his father, riding his bike, making goofy jokes, and playing baseball.
He said he heard that about a week before the Jan. 10 incident that his son had bullying issues with the boy who allegedly punched him. He said some other parents have said their children have had bullying problems at the school.
Officials with the Southeast Delco School District did not return calls for comment.
O'Neill said his son told him one boy pushed him into the boy who allegedly bullied him and punched him. He said his son did not want to fight.
"He was trying to walk away," he said.
He said the fight occurred in the late morning, but his son's mother did not learn of it until about 3 p.m. Initially he said his son's nose, which was broken, was checked at a local hospital. Soon afterward, he said, the boy began experiencing mood swings, fatigue, and memory problems.
About two weeks after the incident, the younger O'Neill was put into a medically induced coma at Nemours/Alfred I. duPont Hospital for Children in Wilmington. About two weeks later, he was moved to Children's, his father said.
On Monday, counselors were at the school to help students and staff deal with Bailey's death.
"Our school community is deeply saddened by this loss. Our condolences are with Bailey's family and friends during this very difficult time," Stephen Butz, Southeast Delco superintendent, said in a letter on the district's website.
Butz said the district was cooperating with Darby Township police, who were investigating.
Officials have not released details of the altercation, or directly connected the seizures with the schoolyard incident.
The Rev. Thomas Sodano, pastor of St. Joseph's, said Bailey O'Neill was to be confirmed by Bishop John McIntyre with the other students in his religious instruction class on March 18.
Instead, he administered the sacrament to the boy in his hospital room last week after an MRI showed brain damage. Bailey O'Neill was conscious, no longer in the induced coma.
The priest said the boy's father had a birthday celebration at the hospital on Saturday, the same day, Sodano said, that he administered last rites. He was conscious then, too.
"When I gave him last rites on Saturday, he was looking at me and reaching for me," the priest said.
Sodano said a girl who had told him she witnessed the playground altercation also said O'Neill was backing away and was not looking to fight.
"Anybody who knows him knows he's not that kind of a kid," the priest said.
O'Neill was remembered extensively on Facebook, where a page was created in his honor after the incident became widely publicized.
"First of all, I want to say the battle isn't over. ... We will remember Bailey always and we will continue this fight until Bullying is eradicated," said a post on the Prayers for Bailey O'Neill Facebook page, not run by the family.
His father has set up a "Battle for Bailey" Facebook site.
Posting to the "Prayers" page, football player Ray Rice of the Baltimore Ravens said he had reached out to the boy's family. He vowed to fight against bullying.
"Bailey - my little buddy, I will not let you become just another bully statistic ... you are my inspiration and one more angel that will help me continue the fight for kids everywhere," he wrote. "You are going to help me save lives. RIP my little friend."
Contact Rita Giordano at 610-313-8232, email@example.com or on Twitter @ritagiordanno.
Philly.com staff writer Frank Kummer contributed to this article.