The newspaper announced on Tuesday that Jurgensen would retire at age 55, and that the search for another editor is under way. Craig Moon, the newspaper's publisher, said in a statement to USA Today's staff that Jurgensen's departure "opens the door to move the USA Today brand forward under new leadership."
Some kind of shakeup at USA Today's top level had been anticipated after a panel of three veteran newspaper editors delivered a report to Moon on Kelley's fabrications, which included recommendations for how to prevent a recurrence of similar transgressions.
Both Jurgensen and Kelley, 43, had been at the paper for 21 years, since its launch.
Moon has not yet released any details about the report's contents or its recommendations. He has said he plans to do so some time this week.
Kelley resigned under pressure in January after admitting to trying to deceive editors checking into the veracity of some of his reporting. A subsequent inquiry found that he made up major parts of at least eight stories and committed several acts of plagiarism.
Steven Anderson, a spokesman for the newspaper, said the paper would not have any comments on the departure beyond a brief statement that Moon sent to USA Today staffers late Tuesday.
The scandal deeply embarrassed USA Today, which fought for years to overcome perceptions that it gave serious news topics short shrift with brief news articles and catchy headlines. The newspaper is the largest-circulation daily in the United States and also the flagship publication of Gannett Co., the nation's biggest newspaper publisher.
"Like all of us who worked with Jack Kelley, I wish we had caught him far sooner than we did," Jurgensen said in the announcement to the paper's staff. "The sad lessons learned by all in this dreadful situation will make USA Today a stronger, better newspaper."
In over two decades at the newspaper, Kelley rose to become a globetrotting foreign correspondent reporting from various hot spots. He co-authored two books with USA Today founder Al Neuharth.
Kelley spoke to various groups on behalf of USA Today, and the newspaper nominated him for the Pulitzer Prize five times. He is married to the paper's top advertising executive.
The debacle at USA Today has parallels to a plagiarism scandal last year at The New York Times involving Jayson Blair, who plagiarized or fabricated dozens of stories. The Times' top two editors resigned in the aftermath of that scandal, which exposed deep tensions in the paper's newsroom.
A lawyer representing Kelley did not respond to a request for comment.
As the scandal over Kelley developed, several USA Today reporters said they had raised doubts about the reliability of some of Kelley's dispatches. One of the areas addressed by the inquiry into Kelley's work was the extent to which USA Today's editors might be held accountable for his transgressions.
Tom Squitieri, reporter at the paper since 1989, said he and his colleagues are sad to Jurgensen go.
"We expected people to leave because of the Kelley debacle, and as editor, people could say it happened on her watch," Squitieri said. "She was a well-liked and respected individual, but I understand why she retired."
Executive editor Brian Gallagher, who is in charge of the paper's day-to-day operations, said in a statement: "I don't know anyone at this newspaper who won't be saddened by Karen's departure. Both personally and professionally it is a great loss."
By Seth Sutel