The couple confirmed they had made the ‘difficult decision to divorce’ in a statement.
"After much thought and careful consideration, we have made the difficult decision to divorce," the statement read.
"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."
‘Gone Girl’ star Ben, 42, and Jennifer, 43, have three children together - nine-year-old Violet, six-year-old Seraphina and three-year-old Samuel.
Ben, who plays Batman in the forthcoming ‘Batman vs Superman’, first met Jennifer on the set of the 2003 flop ‘Daredevil’ and the pair started dating shortly after.
Last week, removal trucks were seen outside the family home, amid rumours that the couple were on the verge of a split.
Last month, the US version of OK! magazine claimed that the couple were on the rocks, with a source reportedly telling them that Ben and Jennifer were “already separated”.