Authorities did not immediately explain how 47-year-old Sgt. Steven Floyd died, but the head of the guards union said the 16-year veteran of the prison was forced into a closet and killed by his captors at some point.
Sgt. Floyd, a father of three adult children and a member of the State of Delaware's Prince Hall Masons, is being hailed as a hero by both his co-workers and officials.
RAW VIDEO: Procession for body of Sgt. Floyd
He was one of four hostages being held. Two of them, both corrections officers, were released safely overnight.
The final captive, a female counselor, was safely rescued minutes after the tactical teams forced their way into the all-male, 2,500-prisoner James T. Vaughn Correctional Center shortly after 5 a.m.
"She was not injured in this ordeal, and I would go as far to say that there were inmates that actually shielded this victim," said Delaware Homeland Security Secretary Robert Coupe.
VIDEO: Corrections commissioner describes how standoff ended
Gov. John Carney called the uprising a "torturous" ordeal. In a statement, he said authorities will hold accountable those responsible and "make whatever changes are necessary to ensure nothing like it ever happens again."
"My prayers all day yesterday was that this event would end with a different result but it didn't," Gov. Carney said. "So today all of us mourn for the family of Sgt. Floyd."
During the takeover, Floyd yelled to other guards who were coming to help him that the inmates had set a trap, saving some of his fellow officers' lives, said Geoffrey Klopp, union president.
"Sgt. Floyd was a great man. Even in his last moments, as the inmates attempted to take over the building, Sgt. Floyd told a couple of the lieutenants to get out of the building, that it was a trap," Klopp said Thursday afternoon. "Sgt. Steven Floyd Sr. saved lives in an emergency situation."
The uprising began around 10:30 a.m. Wednesday when inmates with homemade weapons overpowered staff members, seized Building C and took three guards and a counselor hostage.
During negotiations conducted for a while via an officer's walkie-talkie, the inmates released two hostages and got authorities to turn the water back on, saying they needed it for drinking and washing. Instead, they filled up metal footlockers and built barricades at the building's entryways.
Officers finally went in with heavy equipment and found Floyd unresponsive, authorities said. He was pronounced dead about a half-hour later.
The guards who were taken hostage were beaten severely by their captors and suffered broken bones, cuts and an eye injury, Klopp said. Authorities said their injuries were not life-threatening.
It wasn't immediately clear how many inmates took part in the uprising. About 120 were in the building when it began, but dozens were let out as the standoff dragged on.
Officers inside the cellblocks are not armed, for fear they could be overpowered and stripped of their weapons. Armed guards are posted in prison towers.
The negotiations via walkie-talkie were broadcast online for more than an hour before officials blocked the transmission. The conversations were mostly calm, with moments of tension. At one point, an unidentified inmate told a negotiator that the prisoners wanted a "formal apology" from the governor for "decades of oppression."
LISTEN: Exchange between inmate, negotiator in Del. prison hostage situation
The prison, about 15 miles outside the state capital of Dover, holds minimum-, medium- and maximum-security prisoners serving sentences, along with Kent County detainees awaiting trial, and has about 1,500 guards. Building C includes inmates being disciplined for infractions.
While authorities investigate what went wrong, Delaware Homeland Security Secretary Robert Coupe noted the prison system faces staffing shortages every day.
"Statewide, we are down on any given day about 90 positions," said Coupe, who added that the agency uses overtime to meet minimum staffing levels.
Klopp said Floyd's death was preventable and slammed the state for understaffing and low pay.
In 2004, an inmate at the prison raped a counselor and held her hostage for nearly seven hours before he was killed by a department sharpshooter. Klopp said none of the resulting recommendations for improving staffing were put into effect.
According to the department's website, the prison is Delaware's largest correctional facility for men, with about 2,500 inmates.
It employs 1,500 corrections officers, according to Bruce Rogers, counsel for the Correctional Officers Association of Delaware.