Divers found a body "intact" that they believe to be the two-year-old, who was dragged into the water on Tuesday evening in front of his family.
Orange County Sheriff Jerry Demings said the missing boy's name was Lane Graves from Nebraska.
After the attack, five alligators were seized and killed in an attempt to find the boy's remains.
The body found in the water has yet to be formally identified but police are confident it is Lane's.
Earlier on Wednesday, police said there was "no question" the boy was dead.
Some 50 people were using sonar equipment to search a system of lakes and ponds linked by canals to the Seven Seas Lagoon where the boy was attacked while wading in shallow water.
The family with three children from Elkhorn in Nebraska were relaxing near the shore of the lagoon when the incident happened.
There is a "no swimming" sign on the man-made lagoon but although the boy was on the edge of the water, there was no indication he was swimming, Mr Williamson said earlier.
His father sustained minor lacerations to his arm in the attempt to retrieve his child, he added.
No signs around the lagoon warn visitors about the presence of alligators, a situation which a Disney spokesperson told Reuters news agency would be reviewed.
Read more: How often do alligators attack people?
Police searching for a young boy seized by an alligator at Walt Disney World in Florida have recovered a body.