The New York Times took away two Pulitzers, and the committee notably did not make awards for editorial writing or fiction.
His AFP photograph published December 7 shows young Tarana Akbari screaming after a suicide bomber detonated a bomb in a crowd at the Abul Fazel Shrine in Kabul on December 6.
"When I could stand up, I saw that everybody was around me on the ground, really bloody. I was really, really scared," said the girl, whose name means "melody," and whose age has been given as either 10 or 12.
Sig Gissler, the Pulitzer administrator, called the AFP picture "one single riveting photograph," and "a picture you will long remember."
Gissler also said the awards highlighted the changes in the media landscape by recognizing more online news operations.
David Wood of The Huffington Post won the national reporting prize "for his riveting exploration of the physical and emotional challenges facing American soldiers severely wounded in Iraq and Afghanistan," the committee said.
The Pulitzers, which date back to 1917, began allowing online-only publications to compete three years ago.
Politico's Matt Wuerker won the award for editorial cartooning, satirizing the partisan conflict that engulfed Washington during 2011.
The public service award went to The Philadelphia Inquirer "for its exploration of pervasive violence in the city's schools," according to the Pulitzer committee.
The prize for breaking news went to the staff of the Tuscaloosa News for the Alabama newspaper's coverage using real-time updates to help locate missing people after a deadly tornado, which forced the paper to publish at another site.
The award for investigative reporting was shared by Matt Apuzzo, Adam Goldman, Eileen Sullivan and Chris Hawley of the Associated Press and Michael Berens and Ken Armstrong of The Seattle Times.
The AP was recognized for reporting on the New York Police Department's clandestine spying program that monitored daily life in Muslim communities.
The Seattle Times journalists were honored for their coverage of a little-known governmental body in Washington state which moved vulnerable patients from safer pain-control medication to methadone, a cheaper but more dangerous drug.
The New York Times took awards for explanatory reporting for David Kocieniewski's coverage of tax loopholes; and for international reporting for Jeffrey Gettleman's coverage of famine and conflict in East Africa.
Pulitzers also went to Sara Ganim and members of The Patriot-News Staff in Harrisburg, Pennsylvania, for local reporting; Eli Sanders of the Washington state weekly The Stranger, for feature writing; Mary Schmich of the Chicago Tribune for commentary; Wesley Morris of The Boston Globe for criticism; and Craig Walker of The Denver Post for feature photography.
Besides journalism, the Pulitzer Board, made up of journalists from around the country and representatives of New York's Columbia University, also hands out awards for literature, drama and music. No award was made this year for fiction.
The drama award went to "Water by the Spoonful" by Quiara Alegria Hudes, while the history prize went to the late Manning Marable for "Malcolm X: A Life of Reinvention."
John Lewis Gaddis won the Pulitzer for biography for his book "George F. Kennan: An American Life," on the American diplomat.
The Pulitzers for poetry went to "Life on Mars" by Tracy K. Smith; general nonfiction to "The Swerve: How the World Became Modern," by Stephen Greenblatt; and music to "Silent Night: Opera in Two Acts" by Kevin Puts.
Each Pulitzer winner receives $10,000.
