The Times-Picayune of New Orleans received the Pulitzer Prize for Breaking News Reporting.
It also shared the Pulitzer Prize for Public Service with The Sun Herald of Biloxi, Mississippi, for their handling of the August 29 storm and aftermath.
The 90th annual Pulitzer Prizes in Journalism, Letters, Drama and Music were announced by Columbia University in New York City on Monday.
Sig Gissler, Pulitzer Prize administrator, said: "The board regards this as extraordinary work by two papers ... in the aftermath of Katrina, which is considered the nation's worst natural disaster."
The storm battered hundreds of miles of the US Gulf Coast, killing about 1,600 people and leaving hundreds of thousands homeless.
In New Orleans, 80% of which was flooded, most businesses have not reopened and many residents have not returned.
Complaints have persisted that the federal government has failed to provide adequate relief.
The two award-winning newspapers provided their coverage even as they suffered from the storm's wrath.
Editor Jim Amoss congratuled his
team at the Times-Picayune
The New Orleans paper's offices were flooded, and many of its staff were forced to flee when the city's levees gave way.
A makeshift newsroom was set up in Baton Rouge, Louisiana, about 130km away.
News of the prizes evoked tears and cheers from the reporters, editors and family members who gathered in the Times-Picayune newsroom in anticipation of the celebration.
Jim Amoss, the editor, said: "We have an extraordinary team of journalists and employees in this company who are absolutely dedicated to getting this paper out, no matter what the conditions are, people who lost their homes, who didn't know what had become of their families and who kept on working."
Biloxi's Sun Herald won "for its valorous and comprehensive coverage of Hurricane Katrina, providing a lifeline for devastated readers," the Pulitzer Board said.
The Public Service award is considered the most prestigious.
Domestic, global issues
For photographs that "depicted the chaos and pain" of the hurricane, The Dallas Morning News won the Pulitzer Prize for Breaking News Photography.
The Washington Post won four Pulitzers, the most of any newspaper this year.
This photo of a US Marine's casket
being unloaded was awarded
The prize for Investigative Reporting went to the Post's Susan Schmidt, James Grimaldi and R Jeffrey Smith for their inquiry of Washington lobbyist Jack Abramoff that exposed corruption and prompted reform efforts.
The Pulitzer for Explanatory Reporting went to The Post's David Finkel for his case study of the US government's attempt to bring democracy to Yemen.
The Post's Dana Priest won the prize for Beat Reporting for coverage of secret prisons and other controversial features of the Bush administration's counterterrorism campaign and the Pulitzer for Criticism went to Robin Givhan for her writing about fashion.
The Pulitzer for National Reporting was shared by The New York Times' James Risen and Eric Lichtblau for articles on secret domestic eavesdropping and the staffs of The San Diego Union-Tribune and Copley News Service, with notable work by Marcus Stern and Jerry Kammer, for their disclosure of bribe-taking that sent former US Representative Randy Cunningham of California to prison.
Also at The New York Times, the prize for International Reporting went to Joseph Kahn and Jim Yardley for stories on justice in China.
Nicholas Kristof won in the category of Commentary for columns on genocide in Darfur.
An editorial cartoon with names
of soldiers killed in Iraq
For Feature Writing, Jim Sheeler of the Rocky Mountain News in Denver won for his story on a Marine major who helps families of comrades killed in Iraq.
The Rocky Mountain News' Todd Heisler won for Feature Photography for his behind-the-scenes look at funerals for Marines who return from Iraq in caskets.
The Oregonian's Rick Attig and Doug Bates won for their editorials on abuses inside a forgotten Oregon mental hospital, while the prize for Editorial Cartooning went to The Atlanta Journal-Constitution's Mike Luckovich.
In the arts categories, the fiction prize went to March, Geraldine Brooks' novel imagining the life of the father in Louisa May Alcott's Little Women.
Caroline Elkins won in general nonfiction for Imperial Reckoning: The Untold Story of Britain's Gulag in Kenya.
The Pulitzer for poetry went to Claudia Emerson, a 49-year-old English professor at the University of Mary Washington in Fredericksburg, Virginia, for her book of poetry Late Wife.
Claudia Emerson won for her book
of poetry, titled Late Wife
It was a collection handwritten letters reflecting on her failed marriage of 19 years and her blossoming relationship with her second husband.
Despite as many as 100 drama entries, none gained a majority vote of the 18-member Pulitzer board, and so it did not issue a drama award for the first time since 1997.
"There was no clear-cut winner," Gissler said.