The couple made the sad revelation just one day after their 10-year wedding anniversary.
In a statement to People magazine, they said: "After much thought and consideration, we have made the difficult decision to divorce.
"We go forward with love and friendship for one another and a commitment to co-parenting our children whose privacy we ask to be respected during this difficult time.
This will be our only comment on this private, family matter. Thank you for understanding."
Last month US reports claimed that the much loved couple had already separated, with Ben's alleged gambling causing strain on the relationship.
A source told OK! USA: "Ben wants the official statement to come out a few weeks before their 10th anniversary – which he hopes will give enough time for the news to die down by the time he has to promote Batman v Superman and the other movies he has coming out next year."
Ben 42, and 43-year-old Jennifer met in 2003 and got married in 2005. They are parents to Violet, nine, Seraphina, six, and three-year-old Samuel.