Jones is expected to receive a seven-figure financial settlement from the team, but officials said in a statement that the terms of his departure would remain confidential and no further comment would be made on his resignation.
In a statement, Jones said he was resigning because of health concerns - even though Packers executives cited vague "management concerns" that didn't seem to be health-related when Jones took a leave of absence from the team in May, just days before he was to take Harlan's place as the Packers' top executive.
Jones had open-heart surgery in June 2006, but had gradually returned to his duties as the Packers' No. 2 executive by the end of last season. Jones said he had an aortic dissection, a previously undetected rare birth defect of the heart.
"I am grateful that I survived," Jones said. "However, like many heart surgery patients, I have found that the residual effects of the surgeries have made it difficult to continue my current job."
Jones, whom Harlan hand-picked to groom as his successor in 1999, said he was proud of his accomplishments in Green Bay and said he appreciated that the Packers were "fair" to him in his departure.
"The Packers mean so very much to me, but my family means more," Jones said. "I need to put my health and continued recovery above everything else."
Packers executive committee chairman Peter Platten said that it "has become clear" that Jones' leave of absence was caused by his medical situation.
"Both John and the Packers wanted to take the necessary time to evaluate the appropriate course, and we appreciate the professionalism with which he has handled this matter," Platten said in a statement. "At no time have we questioned his integrity or character."
But concerns about Jones' health didn't seem to be on Harlan's mind in May, when he said that several Packers employees had come forward with concerns about Jones in recent months, both from the team's administrative and football staff.
"I had had some incidents myself with John, so I knew that a problem existed," Harlan said in May. "But I wanted the staff to let me know what its everyday workings were, and when those problems continued to exist, I thought it was time to go to the executive committee."
But if any such concern was reiterated on Friday, it wasn't in public.
"We thank John for all his contributions to the Green Bay Packers, and we wish him and his family well," Platten said. "We want to emphasize that John's departure from the Packers is a result of his medical situation. The team accepts his resignation with regret, understanding that family and health must come first. The Packers will always value John for his character, his integrity and his many accomplishments during his eight years of management leadership with the team."
Harlan and other Packers officials weren't available for comment. Jones hasn't spoken publicly since his leave of absence was announced.
The Packers have formed a search committee to select the organization's new chief executive officer, and the search process was discussed at a Wednesday meeting of the team's Board of Directors.
Packers vice president of finance and general counsel Andrew Brandt is considered a leading candidate to take over for Harlan, who will stay on until a new executive is chosen. But the Packers have hired a Chicago-based executive search firm, Spencer Stuart, to assist in the search process - a sign that outside candidates will be considered.
Harlan originally hired Mike Reinfeldt to groom as his successor and still speaks fondly about his former protege. But Reinfeldt left Green Bay to go to Seattle with coach Mike Holmgren, and recently became the general manager of the Tennessee Titans - perhaps placing him off limits for the Packers.
"We've formed a search committee to begin the process of selecting a new CEO for the Packers," Platten said. "On behalf of the Board of Directors, our role will be to conduct a thorough search to select a person of outstanding ability to continue strong leadership of this unique and historic franchise."
The Packers' search committee will consist of six members of the team's executive committee and five other members of the team's board of directors. Harlan and John Underwood, a former member of the executive committee and team treasurer, will serve as consultants for the search.