In October 2003, his conviction was overturned by the Pennsylvania Superior Court, his attorney Eric Weisbrod said.
On Wednesday, Judge John R. Walker accepted Jefferson's no contest plea and sentenced him to 21/2 to five years in prison.
Between the time of his first sentencing and being released on bail last year pending a new trial, Jefferson had already served five years and nine days in prison, court records state.
Green was killed on West Catherine Street in Chambersburg during an argument involving Jefferson's girlfriend, Gayle Jones, and another man who rented property from her. Jefferson testified at his 1999 trial that Green began arguing with one of his other companions and then went inside a house.
Jefferson testified Green then came out of the house and was walking down the street when he turned and pointed a handgun at him.
Much of the prosecution's case rested on the testimony of two eyewitnesses who testified Green was unarmed. Those witnesses, however, had previously been convicted of crimes involving dishonesty or false statements, Weisbrod said.
That information was introduced at trial, but the three-judge superior court panel ruled Jefferson's trial lawyer should have asked the judge to instruct the jury as to how that was relevant in evaluating the witnesses' credibility.
Franklin County District Attorney John F. Nelson said police in Chambersburg had reviewed the case and tried to contact witnesses, but the involvement of one of the prosecution witnesses in other crimes since the shooting would further taint the person's credibility.
Nelson said police were unable to contact any members of Green's family to discuss the issue of retrying the case.
"I did everything a good citizen should," Jefferson told Walker, saying he turned himself and the gun over to police within minutes of the shooting.
"I didn't commit this terrible, wicked deed" of shooting an unarmed man, Jefferson said. He said Green's gun was removed from the scene when a large crowd gathered on the street after the shooting.
"By golly, it sounded like the Old West down there," Walker said.
Had he been retried, Jefferson said the defense had new witnesses willing to testify that Green appeared to be armed. That would have supported testimony in the first trial that the prosecution witnesses were taking drugs, jewelry and other items from Green's body, he said.
"They literally robbed this guy as he was lying on the sidewalk," Jefferson said outside the courtroom.
At the time of his death, Green had drug delivery and possession charges pending against him, according to court records. Less than four months before he was killed, Green was wounded in a drive-by shooting in the borough, court records stated.