Emerging out of the meeting held in the map room of the White House, officials representing the Dalai Lama said the US President shared "genuine concerns" about human rights in Tibet.
After the meeting, the Dalai Lama said Obama is the president of the greatest democratic country, so naturally he is showing concern about basic human values, human rights, religious freedom.
"This meeting underscores the President's strong support for the preservation of Tibet's unique religious, cultural and linguistic identity and the protection of human rights for Tibetans," the White House said in a statement.
Obama last met the Dalai Lama in February 2010. Saturday's meeting was scheduled to be held at the map room of the White House and not his Oval office. The meeting was closed for the press.
"The president will highlight his enduring support for dialogue between the Dalai Lama's representatives and the Chinese government to resolve differences," the White House said.
The Dalai Lama, who is living in exile since 1959, says he is peacefully seeking rights for Tibetans and accepts Chinese rule. But China insists that he is a "splittist" bent on dividing the country.
"The meeting is an opportunity to deepen the relationship between the American and Tibetan peoples and for the president to reaffirm US," Mary Beth, president of the International Campaign for Tibet, said ahead of the meeting.
"Support for Tibetan issues, including the Dalai Lama's efforts to reengage the Chinese government in meaningful dialogue on genuine autonomy for Tibetans within the People's Republic of China," Beth said.
Earlier in the day, China reacted strongly to Barack Obama's invitation to the Dalai Lama and said it was firmly opposed to any such move. It had also asked the US president to call off the meeting.
The White House announcement to invite the Dalai Lama comes just two days before the Dalai Lama concludes his 10-day visit to Washington, where he has been presiding over a major Buddhist teaching, the Kalachakra.
During his time in Washington, the Dalai Lama met with Speaker of the House John Boehner, Democratic Leader Nancy Pelosi, the Senate Foreign Relations Committee Chairman, John Kerry, as well as other officials and dignitaries.
