It was Obama's fourth meeting with the Dalai Lama, each of which led to displeasure in Beijing. A White House official said ahead of the talks that the pair would discuss a range of issues, including human rights, but declined to provide any further details about the meeting, which was not open to the press.
Afterward, the White House said the Dalai Lama extended condolences for Sunday's terror attack in Orlando, but declined to provide further details of the discussion.
The Dalai Lama officially retired in 2011 from his political role as the leader of the exiled Tibetan government, but remains the head of Tibetan Buddhists and the object of scorn from the Chinese government.
Before the session at the White House was even announced, a Chinese foreign ministry spokesman sharply criticized any decision that could lend legitimacy to the Dalai Lama's claims that Tibet should be independent from China.
"The U.S. government made solemn commitments. It acknowledges that there is only one China, that Tibet is an inseparable part of China and will never recognize the so-called Tibetan government in exile," the spokesman, Lu Kang, said during a daily press briefing Tuesday.
"Under the cloak of religion, the 14th Dalai Lama peddles his political ambitions of dividing China all around the world," the spokesman added. "We ask all countries and governments not to give him any room to carry out such campaigns, even less risking arousing the firm opposition from the 1.3 billion Chinese people."
Nationalistic Chinese state-run tabloid Global Times said the meeting showed Obama's "mean side."
"While Obama often says he welcomes China's peaceful rise, his meetings with the Dalai Lama erode his sincerity and make him look more like he is helping the latter continue to make trouble with China," the paper said in an editorial
Obama and the Dalai Lama met in the Map Room, on the ground floor of the White House residence. Obama and previous presidents have avoided receiving the Dalai Lama in the Oval Office, a setting typically reserved for visiting heads of state or government leaders.
Josh Earnest, the White House Press Secretary, said Wednesday the meeting's venue indicated that it was a personal greeting rather than formal bilateral talks.
Earnest stressed the meeting with the Dalai Lama didn't reflect a change in official U.S. policy, which currently does not support an independent Tibet.
"Tibet, per U.S. policy, is considered part of the People's Republic of China," Earnest said, noting Obama's "warm personal feelings" for the Dalai Lama and his support for "preserving Tibet's unique religious, cultural, and linguistic traditions."
Any change in U.S. policy toward Tibet could have withering effects for the U.S.-China relationship, which is delicately balanced between areas of cooperation and deep disagreements.
Washington and Beijing are cooperating on a climate agreement, and have coordinated sanctions against North Korea over the country's nuclear provocations.
But maritime disputes in the South China Sea, currency disagreements and concerns over human rights remain persistent sticking points in the relationship.