Mr Obama greeted the Tibetan spiritual leader, who lives in exile in India, a fellow Nobel laureate, who is in the US on a speaking tour.
The meeting was closed to photographers, and, unlike some previous visits, the Dalai Lama left the White House without speaking to reporters.
In a statement after the meeting, the White House said Mr Obama offered his “strong support for the preservation of Tibet’s unique religious, cultural, and linguistic traditions” and for human rights protections for Tibetans in China.
The Dalai Lama told Mr Obama he is not seeking Tibetan independence, and both leaders said they hoped talks would resume between Beijing and the Dalai Lama’s representatives. Tibet has been occupied by the Chinese since 1951 and was deprived of its autonomous identity after a failed uprising in 1959.
When the White House announced the meeting on Thursday night, China responded almost immediately, urging Mr Obama to cancel it in what has become something of a diplomatic ritual whenever the president meets with the exiled Buddhist monk. In a statement, China’s government accused Mr Obama of letting the Dalai Lama use the White House to promote anti-Chinese activities.
“It is a severe violation of the principles of international relations,” said Hua Chunying, a spokeswoman for China’s foreign ministry. “It will inflict grave damages upon the China-US relationship.”
Beijing has often protested when world leaders have granted audiences to the Dalai Lama, including when Mr Obama met him in 2010 and again in 2011. Chinese officials denounce the Dalai Lama as a separatist responsible for instigating self-immolations by Tibetans inside China, but he is respected for his advocacy of peace and tolerance.
Mr Obama hosted the Dalai Lama in the White House’s Map Room, rather than the Oval Office, where the president traditionally brings a visiting leader for a photo opportunity. The private meeting, closed to reporters despite media requests for access, suggested an attempt to avoid the appearance of a meeting between heads of state.
The White House said Mr Obama was meeting the Dalai Lama in the visitor’s capacity as a cultural and religious leader. As if to indicate a reaction had been expected, officials reiterated that the US recognises Tibet as part of China and does not support Tibetan independence.
At the same time, officials said they were concerned about tensions and deteriorating human rights in China’s Tibetan areas, urging Beijing to resume talks with the Dalai Lama or his followers without preconditions.
China bitterly opposes the Dalai Lama’s quest for greater Tibetan autonomy and is wary of Obama’s efforts to increase US influence in the region.
Relations between the US and China are already on edge over Beijing’s steps to assert itself in the region, including in territorial disputes with smaller neighbours. China’s emergence as a global power has strained ties with Washington, and the two have also clashed over cybertheft and human rights.
A frequent visitor to the US, the Dalai Lama has lived in exile in northern India since fleeing China in 1959.