The Royal Swedish Academy of Sciences cited Professor Ostrom, who teaches at Indiana University, "for her analysis of economic governance," saying her work had demonstrated how common property could be successfully managed by groups using it.
She told Swedish television that she was "in shock" at being the first woman to clinch the award, adding winning had been a "great surprise".
NOBEL PRIZE WINNERS 2009
Peace: Barack Obama
Physics: Charles K Kao, Willard S Boyle and George E Smith
Chemistry: Venkatraman Ramakrishnan, Thomas A Steitz and Ada E Yonath
Physiology or Medicine: Elizabeth H Blackburn, Carol W Greider and Jack W. Szostak
Meanwhile, Professor Williamson, the academy said, developed a theory where business firms served as structures for conflict resolution.
The University of California, Berkeley academic has argued that hierarchical organisations such as companies represent alternative governance structures, which differ in their approaches to resolving conflicts of interest.
"Over the last three decades, these seminal contributions have advanced economic governance research from the fringe to the forefront of scientific attention," the academy said.
The pair will share the 10-million Swedish kronor (£910,000; $1.44m) prize.
Last year, American academic Paul Krugman won the prize, in recognition of his analysis of trade patterns and where economic activity takes place.
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