Murdoch, 82, married the Chinese-born Wendi Deng, 44, famed for attacking a protestor who hit her husband with a custard pie, in 1999. The couple have two daughters, aged 11 and nine.
The media mogul, whose wealth is estimated $11.2 billion, filed for divorce on the grounds that his relationship with his third wife had broken down “irretrievably for more than 6 months”.
The divorce petition was filed on Thursday in the New York Supreme Court.
Mrs Murdoch was informed in advance of her husband's decision, according to a person close to the family.
The divorce could prove one of the most expensive in legal history.
Murdoch's split from his second wife Anna Maria cost him $1.7 billion, including an $110 million cash settlement, in 1999.
Murdoch and Deng, who met at a Hong Kong company party in 1997, married just three weeks after his previous divorce was finalised.
A pre-nuptial agreement between Murdoch and Deng and two post-nuptial agreements will now be enforced.