She resigned from the job in 2011 amid the phone-hacking scandal at the organisation owned by Rupert Murdoch. However Brooks was cleared of the charges last year following a trial at the Old Bailey.
She replaces Mike Darcey who is leaving the post as chief executive after three years.
Robert Thomson, the chief executive at News Corp said: "Rebekah will lead a great team at News UK into the digital future, while maximising the influence and reach of our newspapers, which remain the most informative and successful in Britain and beyond.
"Her expertise, excellence and leadership will be crucial as we work to extend our relationship with readers and advertisers, and develop our digital platforms to take full advantage of our brilliant journalism."
As part of the leadership changes David Dinsmore, the editor at The Sun, has been promoted to the chief operating officer; and Tony Gallagher, the joint deputy editor of The Daily Mail, has become the editor-in-chief at The Sun.
Brooks said: "I am delighted to return to News UK. It is a privilege to be back amongst the most talented journalists and executives in the business.
"I am confident that we can meet the many challenges of this digital age with a combination of cutting edge technologies and world class journalism."