David Rohde, together with a local reporter, Tahir Ludin, and their driver, Asadullah Mangal, were abducted on November 10 outside Kabul.
The newspaper, quoting Rohde's wife Kristen Mulvihill, said Rohde and Ludin late Friday climbed over a wall of the compound where they were being held in North Waziristan in Pakistan. Mangal did not escape with them, it said.
The two men found a Pakistani army scout who took them to an army base and on Saturday they were flown to the US Bagram military base in Afghanistan, it said.
In a statement, US Secretary of State Hillary Clinton said she was pleased that Rohde's ordeal had ended. "I would like to thank the governments of Pakistan and Afghanistan for their assistance in ensuring his safe return," she said without elaborating.
New York Times executive editor Bill Keller said the newspaper had kept quiet about the kidnapping in order to avoid increasing the danger to the men. He declined to discuss efforts to win their release but said no ransom was paid and no Taliban or other prisoners were released, the paper said.
Rhode, 41, had been in Afghanistan working on a book.
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