The prize was awarded for a novel that imagines the life of a minor character in the American classic Little Women.
It depicts the life of John March the absent father of four sisters growing up in Massachusetts during the American Civil War.
For the first time since 1997 the Pulitzer board's declined to award a prize for drama.
In her novel, John March works as a military chaplain through the war while his wife and four daughters remain in Massachusetts.
The writer said she was "in a state of disbelief, really. I just can't believe it. It's like being struck by lightning. I have no big plans. I think I might have to make some, and they might have to involve some champagne," she said.
Her husband, Tony Horwitz, won a Pulitzer in 1995 for national reporting with The Wall Street Journal.
Geraldine Brooks who has dual Australian and US citizenship was reached in Cambridge, Massachusetts, at the Radcliffe Institute for Advanced Study at Harvard.
Other winners
David M. Oshinsky, a professor of American history at the University of Texas, Austin, was awarded the history prize for Polio: An American Story.
"I grew up in fear of this disease. I remember the iron lung and the wheelchairs and not being able to go to swimming pools," the author said in talking about a subject he said always interested him.
The prize for general non fiction went to Caroline Elkins for Imperial Reckoning: The Untold Story of Britain's Gulag in Kenya.
Kai Bird and Martin J Sherwin have taken the prize for biography for American Prometheus: The Triumph and Tragedy of J Robert
Oppenheimer.
American Prometheus: The Triumph and Tragedy of J Robert Oppenheimer, by Kai Bird and Martin J Sherwin was cited for
biography.
"Oppenheimer was well known for black hole theory," said Bird. "He as a subject was a black hole - extremely enigmatic, complicated."
The book about the father of the atomic bomb occupied Sherwin
for 25 years. "It was a great project for many of those years and for some of those years, a great burden," he said.
"Marty got biography disease - he ended up with over 50,000 pages of archival research. He was drowning in paper at one point," said Bird.
The prize for poetry went to Claudia Emerson for Late Wife, poems based on a series of letters to her ex-husband.
Emerson, a professor of English at the University of Mary Washington in Fredericksburg, Virginia, said she was thrilled and surprised about the award.
"It's about recovery and convalescence," she said. "It means a lot to me, because the book is intensely personal."
The prize for general non-fiction went to Caroline Elkins for
Imperial Reckoning: The Untold Story of Britain's Gulag in Kenya.
The Pulitzer board had listed three finalists for drama: Red Light Winter, Adam Rapp's play about two good friends and their relationships with a young prostitute they pick up in Amsterdam; Miss Witherspoon, Christopher Durang's surreal fantasy about a perpetually suicidal woman who keeps coming back from the dead; and The Intelligent Design of Jenny Chow, Rolin Jones' comedy about a bright yet eccentric young woman who builds a humanlike robot.
Yehudi Wyner has taken the music prize for Piano Concerto:
Chiavi in Mano.