Chester French musician Maxwell Drummey, who married socialite Geldof in August 2008 in a Las Vegas ceremony, filed the legal papers at Los Angeles County Superior Court on Monday.
According to TMZ, Drummey cited "irreconcilable differences" as the reason behind the divorce.
The couple announced their split in February 2009 despite repeatedly denying relationship problems during their 96-day marriage.
Their official statement read: "Our parting is amicable and both of us still respect and care about each other immensely. There were no other people involved in this decision and we both look forward to a future as good friends. Peaches Geldof will continue to split her time between New York and London."
Shortly after their split, a friend of Geldof said that she married Drummey "for a laugh" and got "bored" of him after becoming "besotted" with The Virgins singer Donald Cumming.
Geldof was romantically linked to Eli Roth last year.