Thomson's appointment was approved by a special committee created to oversee the Journal's editorial integrity, News Corp. said. He succeeds Marcus Brauchli, who quit in April.
Murdoch is remaking the Wall Street Journal to include more political and arts coverage to compete with the New York Times. He brought in Thomson, 47, from the Times of London to be publisher of the Journal in December, shortly after taking control of Dow Jones & Co. in a $5.2-billion acquisition.
"Taking readership away from the New York Times is clearly a goal of Murdoch's," said analyst Ken Doctor at media consultant OutSell Inc. in Burlingame, Calif. "Murdoch wants a competitive weapon as well as a solid work of daily journalism."
Class A shares of News Corp. fell 17 cents to $19.09.
Thomson also will be editor-in-chief of Dow Jones, overseeing editorial operations of the company's news wires. He is relinquishing the role of publisher to Dow Jones Chief Executive Les Hinton, 64, who will hold both posts.