The meeting took place in private in Washington, in the White House's Map Room, as opposed to the Oval Office, where the President usually meets international leaders.
The choice of venue has been widely interpreted as an attempt to appease the Chinese government in Beijing, which considers His Holiness to be a separatist and believes that official foreign contact with him infringes on China's sovereignty over Tibet
Emerging from the hour-long meeting, His Holiness told reporters he "very happy" with the session, saying he spoke to President Obama about the promotion of human value, religious harmony, a greater leadership role for women around the world and the concerns of the Tibetan people. He said the President was "very much supportive."
White House press secretary Robert Gibbs said, "The President commended the Dalai Lama's 'Middle Way' approach, his commitment to non-violence and his pursuit of dialogue with the Chinese government."
Washington kept the talks low-key because it does not wish to exacerbate current tensions with China over issues such as US weapons sales to Taiwan, currency policy, trade disputes and internet censorship.
Further, President Obama is seeking to avoid compromise to his efforts to secure China's help in imposing tougher sanctions on Iran and North Korea for their nuclear programmes, and forging a new global accord on climate change.
The Dalai Lama's envoy, Lodi Gyari, said even a private meeting with Obama was a boost for Tibetans feeling marginalized by China.
Michael Green, former President George Bush's senior Asia advisor commented, "The Chinese government is preoccupied with protocol and how things look. The fact that (His Holiness and President Obama) spent time together in an intimate setting means everything for the Tibetan cause."
Predictably, Beijing responded angrily to the meeting. Chinese Foreign Ministry spokesman Ma Zhaoxu said in an official statement, "The behaviour of the US side seriously interferes in China's internal politics and seriously hurts the national feelings of the Chinese people."
He added that the meeting "violated the US government's repeated acceptance that Tibet is a part of China and that it does not support Tibetan independence".
The White House has defended the decision to receive His Holiness, saying he is "an internationally respected religious leader".
His Holiness has met every sitting US President since 1991, with each visit provoking criticism from Beijing.