"A Walk to Beautiful," directed and produced by Mary Olive Smith, focuses on five women who have been shunned by their families and villages but find assistance in a distant women's hospital.
The doc's filmmakers accepted the honor at the IDA's annual awards gala at the Directors Guild of America Theatre in Los Angeles.
Smith's film beat out Michael Moore's "Sicko," Dan Klores' "Crazy Love," Richard E. Robbins' "Operation Homecoming: Writing the Wartime Experience" and Alex Gibney's "Taxi to the Dark Side."
In the short-documentary competition "A Son's Sacrifice," from director Yoni Brook, won the top prize. The film follows Imran, a young American Muslim who confronts his roots at his father's slaughterhouse in New York City.
The inaugural Alan Ett Music Documentary Award for exemplary creative use of music was given to director-producer Paul Taylor for "We Are Together."
Previously announced honors included the presentation of the IDA career achievement award to Michael Moore, who did not plan to attend the ceremony.
The Pare Lorentz Award, given to the film that best represents the activist spirit, went to director-producer Spike Lee for "When the Levees Broke: A Requiem in Four Acts."
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The IDA outstanding documentary cinematography award went to Ken Burns' longtime cameraman Buddy Squires.
Other honorees included CNN's Christiane Amanpour, who received the Courage Under Fire Award, reserved for individuals who put themselves in harm's way to bring important stories to the public.
Paula Apsell, a senior executive producer of PBS' "Nova" series, received the pioneer award in recognition of her significant contributions to advancing the art and future of nonfiction filmmaking.
The preservation and scholarship award was presented to National Geographic Digital Motion; "Darfur Now" director Ted Braun received the Jacqueline Donnet Emerging Documentary Filmmaker Award.
Showtime's "This American Life," created by Ira Glass and Chicago Public Radio, captured the IDA award for a continuing series. The limited series prize went to the PBS program "The Supreme Court," directed by Thomas Lennon.