Zannino became CEO of Dow Jones, which publishes The Wall Street Journal, in early 2006. Dow Jones said in a statement that Zannino's successor would be announced "shortly," and that Zannino would assist in the transition.
Murdoch's deal to acquire Dow Jones for $5.6 billion is expected to close shortly after Dow Jones shareholders vote on it Dec. 13.
Murdoch had faced opposition from several members of the family that controls Dow Jones' shareholder vote and a union that represents Journal reporters, but he convinced enough members of the Bancroft family to support the deal to assure its passage.
The $60 per-share price that Murdoch is paying represented a massive premium of 65 percent what Dow Jones shares had been trading before his offer became public.
At a time of general contraction in the newspaper industry, Murdoch has also said he would invest additional resources in the Journal, expanding its overseas presence, online operations and coverage of Washington.
Zannino had been the first non-journalist to lead Dow Jones in recent memory. Under his tenure, the company reorganized its business units, launched a narrower and redesigned version of the Journal, and took in the other half of the Factiva news database that it didn't already own, buying the stake held by Reuters Group PLC.
In the process, Dow Jones also sold six community newspapers from its Ottaway group to finance the Factiva deal. On Nov. 27, Dow Jones said it was considering selling the remaining papers in the group, consisting of eight dailies and 15 weeklies.
Zannino said in a statement that he had been discussing his departure from the company with Murdoch since September. News Corp. formally announced the deal to acquire Dow Jones on Aug. 1.