The two met in Washington despite Chinese objections.
China has denounced meetings between foreign leaders and the exiled Tibetan Buddhist spiritual leader, whom the country considers a separatist.
The pair, who have met several times before, talked behind closed doors in the White House Map Room.
A Chinese foreign ministry spokesman condemned Wednesday's meeting.
"If the United States plans this meeting, it will send the wrong signal to Tibet independence and separatist forces and harm China-US mutual trust and cooperation," said Lu Kang.
Mr Obama encouraged direct dialogue between the Dalai Lama and China, the White House said.
"Tibet, per US policy, is considered part of the People's Republic of China, and the United States has not articulated our support for Tibetan independence,'' said White House Press Secretary Josh Earnest.
"Both the Dalai Lama and President Obama value the importance of a constructive and productive relationship between the United States and China.
"All of those were policy positions of the United States before the meeting occurred. Our policy hasn't changed after the meeting.''
Mr Obama has previously described the Tibetan Buddhist leader as a "good friend".
The Dalai Lama fled to India after a failed uprising against Chinese rule in 1959.
The Buddhist leader has pushed for more Tibetan autonomy while China accuses him of encouraging outright independence.
US President Barack Obama has met the Dalai Lama in private and told him he encourages dialogue with China, the White House has said.