Dr. Dilip Joseph was freed during an operation in eastern Afghanistan and was being checked out before being reunited with his family, a spokesman for the International Security Assistance Force said.
Joseph had been abducted by Taliban insurgents Wednesday in the vicinity of Sarobi District of Kabul province.
Gen. John R. Allen, commander of U.S. forces in Afghanistan, gave the rescue mission the green light to go forward after intelligence showed the doctor was in imminent danger of injury or death, the ISAF said in a release posted on its website.
"Today's mission exemplifies our unwavering commitment to defeating the Taliban," Allen said.
"I'm proud of the American and Afghan forces that planned, rehearsed and successfully conducted this operation. Thanks to them, Dr. Joseph will soon be rejoining his family and loved ones."
The rescue operation drew praise from President Obama, who said the soldiers' efforts were "characteristic of the extraordinary courage, skill and patriotism that our troops show every day."
The president noted one American died in the operation.
"Tragically, we lost one of our special operators in this effort," Obama said. "Our thoughts and prayers go out to his family, just as we must always honor our troops and military families. He gave his life for his fellow Americans, and he and his teammates remind us once more of the selfless service that allows our nation to stay strong, safe and free."
The New York Times reported at least six people were killed and two Taliban leaders were arrested during the rescue.
The newspaper said Joseph, who is from Colorado Springs, Colo., was with two Afghan men when they were abducted while driving to a rural medical clinic and were taken to a mountainous area about 50 miles from the border with Pakistan. Negotiations led to the release of the two Afghans Saturday, the Times said.