The Control Room, directed by Nujaim and documenting the TV channel during the first days of the war in Iraq, won the North Carolina festival's top prize.
It also garnered the Center for Documentary Studies Filmmaker Award and second prize in the Seeds of War category.
Nujaim, whose first full-length documentary, Startup.com, captured the rise and fall of a dot-com company in the 1990s, told a packed audience at Friday night's screening that she strove to capture the dynamics "of truth - who gets to tell it and how, especially in war".
"The media played a big and vital part in writing the history of this war. All the news outlets had their own audiences to consider and had their own perspectives on how to report," she said.
Nujaim took her camera and tiny crew to Qatar just before the war started, gaining access to both US Central Command headquarters and Aljazeera's offices.
The film follows three main characters: a senior producer at the satellite station focused on creating a truly independent Arab channel with a Western mentality; an Aljazeera journalist who passionately opposes the war while praising the US Constitution; a marine charged with defending the US military operation to the global press.
Magnolia Pictures will distribute the film this summer.