Ms. Brooks, who was editor of The News of the World when the abuses began in 2002, repeatedly told the Murdochs that she knew nothing of the hacking and that she would be exonerated when all the facts came out.

In her farewell message, Ms. Brooks acknowledged that she had become a distraction. “The reputation of the company we love so much, as well as the press freedoms we value so highly, are all at risk,” she wrote. “As chief executive of the company, I feel a deep sense of responsibility for the people we have hurt and I want to reiterate how sorry I am for what we now know to have taken place.”

On Friday, former staff members at The News of the World questioned why Ms. Brooks did not resign earlier. “Our paper was sacrificed to save her career, and now she’s gone as well,” one former employee said, requesting anonymity because he did not want to jeopardize his position in severance negotiations. “Who knows why they’ve chosen to do it now, as she’ll have to appear before the select committee anyway.”

Until Friday, Mr. Hinton had been largely an offstage figure in the scandal. But questions grew about what he knew about the improper practices going on at the newspapers under his watch, even though he has testified twice before Parliament saying that he believed the hacking was limited to one rogue journalist and a private investigator employed by The News of the World.

Letting Mr. Hinton go was an especially fraught decision for Mr. Murdoch. The two had worked together for 52 years, since Mr. Hinton joined Mr. Murdoch’s first paper, The News of Adelaide in South Australia, when he was 15. Moreover, Mr. Hinton ran The Wall Street Journal, Mr. Murdoch’s most cherished American newspaper.

In a note to his employees, Mr. Hinton said Friday was “a deeply, deeply sad day for me.”

Employees at The Journal had mixed reactions to Mr. Hinton’s departure. Alan Murray, a deputy managing editor, wrote on Twitter: “Les Hinton was a great leader, and did much to support the advancement of WSJ in print and digital platforms. He will be much missed.”