The Senate confirmed Vivek Murthy as surgeon general on Monday night as Democrats -- in the final days of their majority control of the chamber -- overcame stiff opposition from the National Rifle Association.
The 51 to 43 vote ends more than a year of uncertainty over Murthy's nomination. Obama had tapped the founder of the pro-Obamacare group Doctors for America for the post in November 2013.
But a confirmation vote had been held up after the gun lobby pointed to a letter Murthy had signed calling for new gun control measures in the wake of the Newtown, Connecticut, school shootings, and promised to score a vote in Murthy's favor against senators in its ratings of how strongly lawmakers support gun rights.
Murthy, 37, is America's youngest-ever top doctor, and he is also the first surgeon general of Indian-American descent.
Obama lauded Murthy's confirmation, saying he will help the United States combat the threat of Ebola.
"As 'America's Doctor,' Vivek will hit the ground running to make sure every American has the information they need to keep themselves and their families safe. He'll bring his lifetime of experience promoting public health to bear on priorities ranging from stopping new diseases to helping our kids grow up healthy and strong," Obama said in a statement.
"Vivek will also help us build on the progress we've made combating Ebola, both in our country and at its source," he said. "Combined with the crucial support for fighting Ebola included in the bill to fund our government next year, Vivek's confirmation makes us better positioned to save lives around the world and protect the American people here at home."
But soon-to-be Senate Majority Leader Mitch McConnell, the Kentucky Republican whose party will take control of the chamber once new members are in place next month, called Murthy a political appointment.
"The surgeon general is known as America's doctor and the men and women chosen to fill that role in the past have usually been highly qualified individuals with substantial experience in patient care," McConnell said in a statement.
"Unfortunately, Dr. Murthy's nomination had more to do with politics -- he was a founder in 2008 of a group called Doctors for Obama, and has been an outspoken political advocate of Obamacare and gun control -- than his medical experience," he said. "With America facing the challenge of Ebola and other serious health challenges, it's unfortunate that the President chose a nominee based on the candidate's political support instead of a long career delivering patient care and managing difficult health crises."