Waller's law office said he died Wednesday, but declined to release other details. Waller died at St. Dominic Hospital in Jackson, where he had been admitted Tuesday night. His family later said he died of heart failure after a short illness.
Funeral services will be held at 2 p.m. Saturday at First Baptist Church in Jackson.
The Mississippi Supreme Court said Waller's body will lie in state from 9 a.m. to 1 p.m. Saturday at the state Capitol in Jackson. Gov. Haley Barbour's office said the governor ordered flags on state buildings to be flown at half-staff starting Wednesday.
Waller, a Democrat, served from 1972-76 — a time when Mississippi governors were limited to one term.
Waller also served as district attorney in Hinds County in the 1960s and twice tried to get a conviction against Byron De La Beckwith for Evers' assassination. In 1994, prosecutor Bobby DeLaughter was able to secure a guilty verdict when blacks were able to serve on the jury.
"Under the circumstances, I think we did the very best job that we could," Waller said in a 2001 interview with The Associated Press "I think the jury was taking the position that they wanted to be convinced beyond a reasonable doubt, to a moral certainty, and a lot of jurors interpret that as eyewitness, direct proof."
Charles Evers, the brother of Medgar Evers, said it's unlikely Beckwith would have been convicted some 30 years later if it weren't for Waller laying the foundation with the two trials in the 1960s.
"He was a true devoted Mississippian who believed in law and order. He believed that if you committed a crime you paid the price. He tried Byron Del Beckwith twice, which was unheard of in those days to prosecute a white man for doing anything to a black man.
"He did everything he could. He just couldn't get a conviction," Evers said.
Waller Jr. said his father's prosecution of Beckwith inspired him to pursue a legal career. "That prosecution made an indelible impression on me and led me to consider law as a career," he said. "It was a watershed event that moved Mississippi toward equal treatment of all people."
Waller Jr. said he practiced law with his father for 20 years. "He knew at some point that I was interested in being a judge and when a position became available he was my avid cheerleader," his son recalled.
"He will be greatly missed. He was a big presence in the legal community, in government and politics in general."
Waller ran an unsuccessful campaign for governor in 1967 but turned things around in 1971, when he rallied against the "Capitol Street" gang that was supporting his opponent. Waller, a Democrat, went on to win the general election over Charles Evers, an independent candidate.
Former Gov. William Winter, who was the lieutenant governor during Waller's administration, said he was saddened to hear a longtime contemporary had died. Winter said Waller was a friend and a successful governor who tried to do what he thought was best for Mississippi.
"He contributed much to the progress of Mississippi. We are all indebted to him for his leadership," Winter said. "Bill Waller was forthright. He was frank, candid. He spoke his opinions in a way that didn't always please people, but he called it just like he saw it."
Barbour said in a statement that "Mississippians have lost a great leader who launched an era of change that continues to this day."
Barbour presented Waller with the Mississippi Medal of Service in 2009.
"He deserved it and more," Barbour said Wednesday.
Waller grew up outside Oxford in a farming family, and hitchhiked to Memphis to get his college education. He earned a law degree back home at the University of Mississippi, married his sweetheart, Carroll, and set up law practice in Jackson.
He returned to that law practice once his term as governor ended — interrupting it to run for the U.S. Senate in 1978 and again for governor in 1987.
The 1971 Democratic primary for governor had a crowded field, with Lt. Gov. Charlie Sullivan as the prohibitive favorite. Waller ran as an outsider, and surprised pundits by capturing the nomination.
In 1973, Waller vetoed funding for a segregationist watchdog agency, the Mississippi Sovereignty Commission, putting it out of business.
Waller appointed the first black member of the state College Board, Dr. Robert Walker Harrison of Yazoo City.
During Waller's administration, Mississippi's three historically black colleges — Jackson State, Alcorn State and Mississippi Valley State — were elevated to university status. Two smaller, predominantly white schools, Delta State College and Mississippi State College for Women, got the same boost.
Waller also concentrated on improving the economy. He spoke proudly of trade missions he led to promote Mississippi products and of other advances his administration pushed for education.
Schools of architecture and veterinary medicine were established at Mississippi State University. A dental school was added to the University of Mississippi Medical Center.
Waller was elected as a Democrat, but didn't remain a party-line man. In 1995, he contributed $2,500 to the re-election campaign of Republican Gov. Kirk Fordice.
Like many other Mississippi leaders, Waller was struck by the limitations of the executive branch in a state where the constitution gives great power to lawmakers. He calls the governorship "a headless horse."
"I'd been in office about three months, legislative leaders approached me and said that the way to govern the state of Mississippi is to cut the ribbons and make the speeches, hold the press conferences and we'll run the government," Waller told the AP. "I told them I was going to hold the office, I didn't care whether they liked it or not."
Waller had little time to enjoy one of the perks of the job. The Governor's Mansion, built in 1841, was in such bad shape that there was talk of turning it into a museum and finding an executive home in the suburbs.
The Wallers led an effort to restore the Mansion as a place for first families to live and ceremonial gatherings to be held. They lived in the house only a few months after it reopened.
"Marsha and I considered him a friend, and our sympathies go out to Carroll and their family. Of course, we have benefited directly from the Wallers' service as they saved the Governor's Mansion from decay and led its restoration," Barbour said. "Today, tens of thousands of Mississippians enjoy this little jewel in downtown Jackson as will generations to come."
Waller is survived by his wife of 61 years, Carroll Overton Waller; four sons, including Mississippi Supreme Court Chief Justice William Waller Jr., and 14 grandchildren.
In lieu of flowers, the family welcomes donations to the Gloria Joy Waller Scholarship Fund at Mississippi College, named after his daughter who died in 1981.