"God of our weary years, God of our silent tears," he said, at the start of his benediction.
Prayers at inaugural ceremonies generally draw little attention, but this year was different. Obama spoke of his faith openly during the election, trying to change the image of the Democratic Party as hostile to religious voters. He has also welcomed nonbelievers, who tend to vote Democratic, in his speeches and public appearances since his earliest days of campaigning.
His supporters had been deeply upset by the prominence of the Christian right during the administration of President George W. Bush, and they watched to see what religious signals Obama would send at his swearing-in.
Warren is a Southern Baptist who wants to broaden the evangelical agenda to include environmental protection, fighting poverty and ending AIDS. He also backed Proposition 8, which banned gay marriage in his home state of California. Gay rights advocates and liberals were outraged that Obama had given Warren a place of honor at the ceremony.
Obama, who prays with Warren, said he wanted the event to reflect diverse views and insisted he remains a "fierce advocate" of equal rights for gays. The new president had also asked Bishop Gene Robinson of New Hampshire, the first openly gay Episcopal bishop, to give the opening prayer Sunday at the inaugural-kickoff event at the Lincoln Memorial.
In his invocation Tuesday, Warren did not refer to the controversy. However, he asked God to forgive "when we fail to treat our fellow human beings and all the Earth with the respect that they deserve." He also prayed for "civility in our attitudes, even when we differ."
Warren said Jesus' name in four languages — English, Spanish, Arabic and Hebrew — and ended his invocation with "The Lord's Prayer," from the Sermon on the Mount.