Brauchli had been in the post for just under a year. He will stay on with News Corp. as a consultant, the company said.
A search for Brauchli's replacement will begin immediately.
Murdoch has been moving quickly to reposition the Journal as a competitor to the New York Times, adding more political coverage and reorganizing the paper.
Meanwhile, Murdoch is close to sealing a deal to buy Newsday from Tribune Co. for about $580 million, a person familiar with the matter said Tuesday.
A deal, long rumored to be in the works, would put Long Island, N.Y.-based Newsday, the New York Post and The Wall Street Journal all under Murdoch's News Corp. media conglomerate.
News of a pending deal was reported late Monday by The Journal, which Murdoch bought last December, and Newsday. The Chicago Tribune, Tribune's flagship paper, also had a similar story Tuesday.
The Journal reported that the deal would be structured as a joint venture in which Tribune Co. would retain a stake of less than 5 percent.
Tribune's new CEO Sam Zell indicated on a conference call last week that he was considering selling Newsday and other Tribune assets, a reversal of his original plan to keep Tribune's businesses largely intact.
Zell said he had been approached by several suitors for Newsday and was considering a sale of the paper, one of Tribune's largest, amid a rapid decline in revenues in the past several months.
Tribune added a heavy load of $8.2 billion in debt as part of a going-private transaction that Zell orchestrated and closed last December.
For Murdoch, gaining Newsday would allow News Corp. to greatly pare down persistent losses at the New York Post, partly by combining back-office and production operations.
The Journal cautioned that many details and tax implications were still being worked out and that the deal could still fall apart.
Any deal for Newsday would be sure to face close regulatory scrutiny since Murdoch's News Corp. already owns the New York Post, the Journal and two New York-area television stations.
A News Corp. spokeswoman didn't immediately return a call seeking comment.