The British newspaper was recognised for "helping through aggressive reporting to spark a debate about the relationship between the government and the public over issues of security and privacy", Columbia University's Graduate School of Journalism said.
The two newspapers shared the Pulitizer Prize in the Public Service category
The Post, meanwhile, was honoured for its "authoritative and insightful reports that helped the public understand how the disclosures fit into the larger framework of national security".
Eli Saslow of the Post will receive the Pulitzer in the category of Explanatory Reporting for articles on the food stamp programme.
In the category of Breaking News Reporting, the jury picked The Boston Globe "for its exhaustive and empathetic coverage of the Boston Marathon bombings and the ensuing manhunt that enveloped the city".
The prize for International Reporting went to Jason Szep and Andrew R.C. Marshall of Reuters for their coverage of the persecution of the Muslim Rohingya minority in Myanmar.
David Philipps of The Gazette, Colorado Springs, Colorado, took the prize in National Reporting for a story about war veterans.
Two photojournalists from The New York Times, Tyler Hicks and Josh Haner, were selected in the categories of Breaking News Photography and Feature Photography, respectively.
The award for Investgative Reporting goes to Chris Hamby of The Centre for Public Integrity.
The prizes, created in 1917 in accord with the will and testament of publisher Joseph Pulitzer (1847-1911), are the pre-eminent honours in US journalism.