The shock announcement comes in the middle of an election campaign in Australia in which the Murdoch media have made clear they want conservative opposition leader Tony Abbott to replace Labor Prime Minister Kevin Rudd.
It also follows the media mogul jetting in his trusted Australian lieutenant, New York Post editor-in-chief Col Allan, last week to shake up his titles.
"Kim has been a steady and courageous leader at a time when our businesses have faced unprecedented pressure and economic challenges," said Murdoch.
Williams took on the job in December 2011, moving from his role as head of Foxtel, a News Corp joint venture that is Australia's largest pay television company.
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It followed a major shake-up during which Murdoch assumed the role of chairman of his Australian arm, which was then called News Limited.
"I am confident that I leave the company in a strong position and with good foundations for the future," Williams said in a statement.
"It has been a privilege to work for News Corp across almost 20 years, and I have no doubt it will remain the most memorable element in my professional commercial life."