Mr Obama praised the Dalai Lama's commitment to nonviolence and "his pursuit of dialogue with the Chinese government," the spokesman said.
Despite American attempts to keep the visit low profile, the Dalai Lama spoke to reporters immediately outside the West Wing of the White House in comments that were broadcast live on international television.
He said he told Mr Obama of his admiration for the US as a "champion of democracy, freedom, human values" and creativity.
The White House had defended the decision to receive the Dalai Lama, saying he was "an internationally respected religious leader".
Mr Obama avoided meeting the Dalai Lama in Washington last year ahead of his own first state visit to Beijing.
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China's foreign ministry quickly condemned the meeting.
Spokesman Ma Zhaoxu was quoted by Xinhua news agency as saying: "The US act grossly violated the norms governing international relations.
"It also went against the repeated commitments by the US government that the US recognises Tibet as part of China and gives no support to 'Tibet independence'."
The foreign ministry had warned the US to call off the Dalai Lama's visit to "avoid any more damage to Sino-US relations".
It said it now expected Mr Obama to take steps to put relations back on track.
China, which sent troops into Tibet in 1950 but has long claimed it as its own, considers the Dalai Lama a separatist. Beijing tries to isolate the spiritual leader by asking foreign leaders not to see him.
The Dalai Lama fled Tibet in 1959 after a failed uprising against Chinese rule and has since been living in India.
Relations between the US and China have become frayed in recent months with US arms sales to Taiwan, a row over internet censorship and US criticisms that China holds its currency artificially weak to boost its exports.
The Dalia Lama has met every sitting US president since 1991, with each visit drawing Chinese ire.
But George W Bush's meeting with the Dalai Lama in 2007 was the first time a sitting US president had appeared in public with the exiled Tibetan leader.
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