Jones, according to an arrest affidavit obtained by The Inquirer, told a witness who came forward last month that Zabel resisted when he rifled his pockets and that his nervous accomplice, Tyrek Taylor, 19, kept asking: "What you doing, Ant?"
Jones displayed the black iPod to friends at a house in Germantown shortly after the killing, explaining that he thought Zabel had an iPhone when he zeroed in on him.
Jones is serving a life sentence on a 2012 murder conviction for shooting Taylor three months after Zabel was killed.
According to the affidavit, Jones told the witness he could not trust Taylor because Taylor was "bitching" about what they had done to "the white boy."
"He had to go," the witness reported Jones as saying.
The new evidence provided the final link for investigators, complementing a statement from a childhood friend of Jones' who told them in 2009 that Jones had talked to him about the killings in prison.
This year, The Inquirer published a series on the fifth anniversary of Zabel's killing.
After police interviewed the new witness last month, detectives requested copies of grainy surveillance footage photos that were published in The Inquirer so they could show them to Jones' family.
On Tuesday, police were arranging for Jones to be transported to Philadelphia from Huntingdon Prison so he could be formally booked in Zabel's death, said Sgt. Robert Kuhlmeier of the Special Investigation Unit, which is handling the case.
That step is expected next week, he said.
Police Commissioner Charles H. Ramsey said he hoped the charges against Jones would provide closure for the Zabel family - and for a city that reeled at the killing.
"It was tragic," said Ramsey, describing what was his first high-profile investigation in Philadelphia. "To be honest with you, it was very embarrassing. He came to this city to help kids and wound up being murdered."
Ramsey said police and prosecutors "never let go of the case" against Jones, a three-time convicted felon from North Philadelphia who was on parole at the time of Zabel's killing.
From a small town in the Midwest, Zabel had chosen Philadelphia because he wanted to teach math in an urban district. Zabel, a teaching fellow who was to start graduate school at Drexel University, was shot once in the neck and died at the scene.
The crime first stumped investigators.
With no witnesses and little physical evidence, there were few solid leads, even with a $35,000, now $55,000, reward and segments on America's Most Wanted.
A month after Zabel's killing, detectives developed their first break when they connected Taylor and Jones to the murder through a cellphone taken in another South Philadelphia robbery.
Prosecutors were able to link the killings of Taylor - who was also shot in the neck - and Zabel through the testimony of Devonne Brinson, who said Jones had spoken to him about the slaying while both were in prison.
While Brinson's testimony allowed prosecutors to establish the connection between the killings, they lacked evidence to charge Jones in Zabel's slaying.
The final break in the case came in October, when detectives received a letter from an acquaintance of Jones who wanted to talk.
The letter led investigators to interview Jones' family, and at least one relative told police that Jones had spoken directly about the Zabel killing.
According to the new affidavit, Jones told the witness and others at the house in Germantown that he and Taylor were out doing a "lick" - a robbery - when they came upon Zabel.
"Give it up," Jones told Zabel.
The way Jones told it, the robbery was fumbled from the start.
For some reason - perhaps because they were on a quiet South Philadelphia street, or because he realized things were going badly - Taylor was startled.
Taylor kept repeating Jones' nickname, so Jones told him to "shut the [expletive] up."
Jones told the group that he pointed his gun at the "white boy" and that Taylor "kept bitching about what was going on."
Jones did not shoot Zabel when he resisted, the witness said. Rather, the witness said, he pulled the trigger when he realized he was not getting much from the stickup.
It was at that point in recounting the crime that Jones displayed the iPod to the people in the house, the witness said.
"He was just a bitch-ass white boy," Jones said.
The new witness' account differs from what police had theorized based on the surveillance footage, which shows only one blurry figure fleeing. Investigators had long believed the person in the video was Jones while Taylor waited in a nearby getaway car.
Jennifer Selber, chief of the District Attorney's Homicide Unit, said her staff wanted to provide Zabel's family justice even though Jones was already serving a life sentence. "We always wanted to make an arrest in this case," she said.
Back in Minnesota, Zabel's mother, Lana Hollerud, said Tuesday that she learned of the charges from a Google alert she had set for news on the case.
She said that she was surprised at how happy she felt - and was thankful to the prosecutors and detectives who seemed to take her son's death so personally.
One of those detectives, George Fetters, said Tuesday he had one final hope for the case:
"That one day the Zabel family will be able to sit in a courtroom and see this guy convicted for taking their son's life."
Read a five-part series about the killing of Beau Zabel and the search for his killer at www.inquirer.com/almostjustice