Divers found the body of Lane Graves about 16 hours after authorities got the call that a reptile had taken the boy from the water’s edge at Seven Seas Lagoon despite his father’s frantic attempt to save the child.
Sheriff Jerry Demings said it appeared the alligator pulled the child into deeper water and drowned him, leaving the body near the spot where he was last seen.
“Of course the family was distraught, but also I believe somewhat relieved that his body was found intact,” Mr Demings told a news conference.
The boy’s parents were identified as Matt and Melissa Graves, of Elkhorn, Nebraska, a suburban area of Omaha. A family friend released a statement on behalf of the couple thanking well-wishers for their “thoughts and hope-filled prayers”.
In a statement from Disney World Resort president George A Kalogridis, the company said it was “doing what we can” to help the family.
Disney World closed beaches around Seven Seas Lagoon during the search.
While “no swimming” signs are posted at the beach where the boy was attacked, no signs warn about alligators. A company representative said it would “thoroughly review the situation for the future”.
Mr Demings said his agency and state wildlife officials would look into the issue of warning signs. He said investigators would also review whether the boy’s parents should be charged, but it is not likely.
“There nothing in this case to indicate that there was anything extraordinary” in terms of neglect by the parents, he said.
Wildlife officials said the attack was a rarity in a state with an alligator population estimated at a million, but it still spooked some visitors in a city built on tourism.
Lane had waded no more than 1ft to 2ft into the water around nightfall on Tuesday when he was taken from a small beach, authorities said.
His father desperately tried to fight off the alligator, suffering lacerations on a hand, but he could not save his son. Neither could a nearby lifeguard, officials said.
No other alligator attacks have been reported on the man-made lake, according to Mr Demings.
The sheriff said the company has a wildlife management system and has “worked diligently to ensure their guests are not unduly exposed to wildlife here in this area”.
Nick Wiley, of the Florida Fish and Wildlife Conservation Commission, said witnesses estimated the alligator was 4ft to 7ft long. Crews removed five alligators from the lake during the search, and officials said one could have been the animal that attacked the boy.
The beach is part of the luxury Grand Floridian resort, across the lake from Disney’s Magic Kingdom theme park. The lake stretches over about 200 acres and reaches a depth of 14ft. It feeds into a series of canals that wind through the entire Disney property.
Though Florida has grown to the nation’s third-most populous state, fatal alligator attacks remain rare. Since 1973, 23 people had been killed by wild alligators in Florida, according to data compiled by the Florida Fish and Wildlife Conservation Commission. The boy makes 24.