Coppola, daughter of Oscar-winning director Francis Ford Coppola, filed divorce papers Friday in Los Angeles County Superior Court. She cited "irreconcilable differences" and said the couple separated in May. They have no children.
The couple reached the decision to divorce "with sadness," Coppola's publicist, Bumble Ward, said in a statement.
Coppola, 32, wrote and directed the recent "Lost in Translation," starring Bill Murray, and the 2000 drama, "The Virgin Suicides."
Jonze, 34, whose real name is Adam Spiegel, is the director of the 1999 cult classic "Being John Malkovich," and last year's "Adaptation."