Authorities said law enforcement officers stormed the underground bunker in Midland City after negotiations with Jimmy Lee Dykes, 65, deteriorated and he was seen holding a gun, the Dothan Eagle reported.
Shortly before 3:30 p.m. EST, two loud bangs were heard emanating from the hostage scene. The noise was followed soon after by an ambulance leaving the scene without its lights or siren activated.
The ambulance traveled to Flowers Hospital where it was believed the freed young hostage, identified only as Ethan, was taken.
Authorities had not disclosed how Dykes died or details of the boy's status, the newspaper said.
"This Wiregrass [region] nightmare is finally over," state Rep. Steve Clouse said. "We're very thankful Ethan is safe and back in the arms of his family. We must still remember the family of Charles Poland [Jr.]. Because of his actions, more than 20 people on that bus are still alive."
The standoff began Tuesday after Dykes got on a school bus in Midland City and demanded Poland, the driver, hand over two children.
When Poland protected the children by blocking Dykes' access to the school bus aisle, the gunman shot the driver four times and grabbed the boy, taking him to his hiding place, police said.
Residents of Midland City had collected birthday cards for the boy, who will celebrate his sixth birthday this week, the Eagle reported Sunday.
Police said there was no previous connection between Dykes, who had a history of animosity with neighbors over perceived transgressions of his property, and the boy. They had not indicated what demands, if any, the hostage-taker may have made.
During the weekend, Dykes allowed authorities to send down medication for the boy's Asperger's syndrome and attention deficit disorder and toys and crackers, CNN reported. Officials said they hoped he would continue to allow them to send comfort items to the boy.
A memorial service was conducted Sunday for Poland and Donny Bynum, the superintendent of Dale County schools, read letters written by children who rode Poland's bus, CNN reported.
"I'm sad to see you gone. You didn't deserve to die, but you died knowing you kept everyone safe," one letter said.
"Charles Albert Poland was a hero," Bynum said.
Officials had been in communication with Dykes through a 60-foot ventilation pipe that leads to the bunker.