Williams is the fourth inmate in a little more than a week to be put to death in Arkansas as the US state rushed to complete a slew of executions before the deadly drugs used in the process expired.
His last meal was fried chicken with barbecue beans and sweet rice.
Williams' final words were, I am "not the same person I was. I have been transformed. Some things can't be undone. I seek forgiveness."
He was due to be killed at 7pm but last minute petitions to the US Supreme Court delayed proceedings.
At 10pm, Mr Williams was informed that the appeals had failed. At 10.52pm a trio of drugs were injected into Williams arm.
Witnesses in the chamber, including an Associated Press reporter, described Williams' movements as "lurching, convulsing, coughing and jerking."
However the state governor has said the execution was "flawless".
A reporter for Arkansas Online, who has witnessed 10 executions, said they had never seen a condemned prisoner move so much while strapped to the gurney.
State news editor Kelly Kissel said three minutes following the drugs being injected, Williams began to cough and gasp. The sound was so loud it was audible even though the microphone was turned off.
Mr Kissel described Williams' movements as "when you're on a bumpy road and you hit a bump."
Williams lurched forward 15 times in a period of 10 to 15 seconds, he said, followed by a slower five lurches as he began "striving for breath. The movements ceased at 10.59pm.
Arkansas Department of Correction spokesman Solomon Graves said Williams shook "for approximately 10 seconds".
A spokesman for Arkansas Governor Asa Hutchinson dismissed the witness accounts and said the lurches were an "involuntary muscular reaction" to one of the drugs used.
Spokesman J.R. Davis stood by his previous description of the state's recent executions as "flawless."
In a written final statement, Williams apologised for his crimes. "I humbly extend my sincerest of apologies to the families I have senselessly wronged and deprived of their loved ones," he said.
"I was more than wrong. The crimes I perpetrated against you all were senseless, extremely hurtful and inexcusable."
After making an oral statement in the death chamber, Williams is reported to have then said he was going to speak in his "native language". Mr Graves said he then began "what would commonly be described as speaking in tongues".
Earlier, Williams ordered his last meal. Like two of the earlier inmates to be executed, he chose fried chicken for his final dinner.
On the tray were two pieces of fried chicken, BBQ beans, sweet rice, corn, bread, two cookies, two cinnamon rolls, and fruit punch.
He also asked for holy communion before the sentence was carried out.
Arkansas Attorney General Leslie Rutledge said she prayed the execution brings "closure and peace to the Boren family," reported Arkansas Online.
"Tonight the rule of law was upheld as the family of Cecil Boren saw justice done.
"On October 3 1999, Cecil was simply going about his daily life at his home near the Cummins Prison Unit when he was shot and killed by an escapee who was serving life imprisonment without parole for capital murder."
In 1998, Williams was sentenced to life without parole after he shot dead Dominique Hurd and almost killed her friend Peter Robertson.
A year later he escaped from the prison in Varner, south of the city of Pine Bluffs.
Williams managed to evade the guards by hiding away in a vat of pig slop as it was ferried from the prison kitchen to a feeding bay, then sneaked along a tree line to escape.
Just a few kilometres from the prison, and still in Varner, he stumbled across Mr Boren tending his garden.
The escapee shot and killed Mr Boren before stealing some guns and making a run for it.
It was while being chased by police that his car ploughed into Mr Greenwood's vehicle killing him.
In 2000, he was sentenced to death for Mr Boren's killing.
The day before he died, Williams received a visit from his daughter and granddaughter. But what is extraordinary about this reunion is was paid for by the family of one of William's victims.
It's an extraordinary gesture many of us might find difficult to comprehend, but Kayla Greenwood said they had forgiven Williams for the death of her father, who was killed in 1999 when the on-the run killer caused a car crash.
Others are less willing to forgive. Genie Boren's husband Carl was killed by Williams when he broke into the couple's home. She says, "people have to be punished for the things they've done."
Mr Greenwood's daughter, Kayla, told the Springfield News-Leader that she learned a few days ago that Williams had a 21-year-old daughter, Jasmine, whom he hasn't seen for 17 years and a three-year-old granddaughter he'd never met.
Ms Greenwood said her mother bought plane tickets for Williams' daughter and granddaughter to fly from Washington state to Arkansas so they could see him on Wednesday, a day before his execution.
"I told him we forgive him and where I stood on it," said Ms Greenwood, who sent a message to Williams through his lawyer.
"When he found out that we are bringing his daughter and granddaughter to see him and that my mum and dad bought the tickets, he was crying to the lawyer."
Members of Mr Greenwood's family had urged clemency for Williams. But family members of Mr Boren told the Arkansas Parole Board that the execution should go forward.
"We've been waiting a long, long time for this. He did a wrong, his jury of peers gave him a death sentence," Mrs Boren told local TV station Fox 16.
