In mid-May, the Casanova actress was awarded £100,000 ($165,000) in damages after she sued the tabloid for hacking her phone.
Earlier today, Michael Silverleaf, a lawyer for the News of the World, extended the tabloid's "sincere apologies" to Miller in London's High Court and agreed to the £100,000 damages, according to the AP.
News of the World also printed an apology for the hacking in April.
A number of other celebrities have also claimed that they were targeted by the newspaper, including Steve Coogan and members of the royal household.
Miller previously sued the tabloid in 2008 for photographing her naked on a closed set. The lawsuit was also settled with an apology as well as damages.
The G.I. Joe actress can be seen next in New Year's Eve, a follow-up to the ensemble film Valentine's Day.