The execution began more than six hours later than intended, and took just 10 minutes.
Franklin declined to make a final statement. Wearing black rimmed glasses with long hair tucked behind his ears, he swallowed hard as five grams of pentobarbital were administered. He breathed heavily a couple of times then simply stopped breathing.
Guards closed the curtains to the viewing area while medical personnel confirmed Franklin was dead.
"The cowardly and calculated shootings outside a St. Louis-area synagogue were part of Joseph Paul Franklin's long record of murders and other acts of extreme violence across the country, fueled by religious and racial hate," Gov. Jay Nixon said in a statement read to reporters by George Lombardi, director of the Department of Corrections, after the execution.
Franklin's lawyer had launched three separate appeals: One claiming his life should be spared because he was mentally ill; one claiming faulty jury instruction when he was given the death penalty; and one raising concerns about Missouri's first-ever use of the single drug pentobarbital for the execution.
But his fate was sealed early Wednesday when the U.S. Supreme Court upheld a federal appeals court ruling that overturned two stays granted Tuesday evening by district court judges in Missouri.
The rulings lifting the stay were issued without comment.
Lori Gresham, Franklin's 34-year-old daughter, said she had spoken to him earlier Tuesday but they did not talk about the execution.
Gresham, the daughter of Frankin's second wife and a resident of Alabama, said she was "really mad about how they went about [the execution]." She was sleeping when she got a call Wednesday about 6:30 a.m. from Franklin's attorneys, telling her he had been executed.
"I did get to say goodbye to him," she said. "I told him I loved him and he told me he loved me. I'm sorry for the families of the victims if they didn't get a chance to do that to their loved ones. I send them my condolences. I'm sorry my dad did all of this. I apologize for my dad and I'm sorry he caused so much hurt and pain in their families. He caused a lot in mine, too."
Franklin was briefly maried twice. Gresham, his only child, was born during the middle years of his killing spree.
One of Franklin's sisters spoke with him about 5:20 a.m. as the state prepared to execute him.
Carolyn Sheffield said Franklin was "chipper. He sounded like he was in a good mood." She said he commented that the execution room was just down the hall from him, but went no further than that.
"I don't think he was afraid to die because he had accepted the Lord," said Sheffield. "He was sorry for everything he'd done."
She said her brother had a tendency to "exaggerate" and she does not believe he committed all the crimes he claimed.
"I just want you to relate a message to Gov. Nixon," said Sheffield, her voice choked with emotion. "Who does he think he is? God has control over life. I don't believe in the death penalty, but he should not have done that after my brother stayed in prison 33 years. The son of a b, that Nixon is. ... he knew better."
Missouri Attorney General Chris Koster said the execution finally meant justice for victims and their families.
"While the sentence that will be carried out today cannot erase the terrible memories of the senseless violence in that synagogue parking lot in October 1977, it does represent a degree of finality for those forever affected by this crime of hate," said Koster. "My thoughts and prayers are with the family of friends of Gerald Gordon."
The family of Martin, one of Franklin's Utah victims, had spent Tuesday preparing for the execution.
Johnnie Mae Martin, his mother, lives in Salt Lake City but is Monticello, Miss., where her son was born and is buried alongside his father.
She planned a ceremony at the Monticello cemetery Wednesday to commemorate her son's life.
Martin's sister, Denna Lightner of Salt Lake City, wrote a letter she hoped was delivered to Franklin Tuesday in which she forgave him for her brother's murder.
Franklin, a paranoid schizophrenic, was in his mid-20s when he began drifting across the country. He bombed a synagogue in Chattanooga, Tenn., in July 1977. No one was hurt, but soon the killings began.
He arrived in the St. Louis area in October 1977 and picked out the Brith Sholom Kneseth Israel synagogue from the Yellow Pages. He fired five shots at the parking lot in Richmond Heights after a bar mitzvah on Oct. 8, 1977. One struck and killed Gerald Gordon, a 42-year-old father of three.
Franklin got away. His killing spree continued another three years.
Several of his victims were interracial couples. He also shot and killed, among others, two black children in Cincinnati, three female hitchhikers and a white 15-year-old prostitute, with whom he was angry because the girl had sex with black men.
He finally stumbled after killing Martin and Fields as the two black men were leaving Liberty Park, where they had been jogging with two white women. He was arrested a month later in Kentucky, briefly escaped, and was captured for good a month after that in Florida.
Franklin was convicted of eight murders: two in Madison, Wis., two in Cincinnati, two in Salt Lake City, one in Chattanooga, Tenn., and the one in St. Louis County. Years later, in federal prison, Franklin admitted to several crimes, including the St. Louis County killing. He was sentenced to death in 1997.
He also admitted to shooting and wounding civil rights leader Vernon Jordan and Hustler magazine publisher Larry Flynt, who has been paralyzed from the waist down since the attack in 1978.
In a Nov. 13 Salt Lake Tribune interview, Franklin said he remained hopeful his sentence would be stayed and that he would have an opportunity to make amends to his victims and work to undo the bad "karma" he had created. "I would be really great to have that opportunity."
He described his own transformation during 33 years in prison as "a miracle."
"I've made an effort to try to change myself and become a better person," he said, mostly by studying world religions.
But in an interview with Fox 2 this week, reporter Tom O'Neal asked Franklin whether he deserved to die for his crimes.
Franklin paused and then said: "To tell you the truth, I actually think I do, yeah. I cannot say no to that question."
Salt Lake Tribune reporter Brooke Adams contributed to this story.