Such meetings in the afternoon are unusual for the tradition-conscious Vatican - most are held at midday. The Vatican clearly sought to accommodate Obama's busy schedule, a sign of Benedict's interest in meeting the American president.
The Vatican has been openly interested in Obama's views, despite his support for abortion rights and embryonic stem-cell research, although some American Catholic bishops have been hostile to his administration.
Benedict broke Vatican protocol the day after Obama was elected, sending a personal note of congratulations rather than waiting to send an official telegram on inauguration day.
L'Osservatore Romano, the Vatican's daily newspaper, gave Obama a positive review after his first 100 days in office, saying in a front-page editorial than even on ethical questions Obama hadn't confirmed the "radical" direction he discussed during the campaign.
Tensions grew when Obama was invited to receive an honorary degree at the leading U.S. Catholic university, Notre Dame. Dozens of U.S. bishops denounced the university and the local bishop boycotted the ceremony.
Yet L'Osservatore concluded that Obama was looking for some common ground with his speech, noting he asked Americans to work together to reduce the number of abortions.
Some conservative American Catholics have criticized the Vatican newspaper for its accommodating stance, and some American prelates at the Vatican have been openly critical of Obama.
Former St. Louis Archbishop Raymond Burke, who now heads a Vatican tribunal, said the U.S. Democratic Party risks becoming a "party of death."
In an interview with an Italian Catholic newspaper, Burke was quoted as criticizing the party for its stands on bioethical issues, especially in defense of abortion rights.
Benedict had a warm relationship with Obama's predecessor, George W. Bush, an abortion opponent, although the Vatican was opposed to the Iraq war.
Polls have shown that Obama received a majority of Catholic votes, especially from the growing number of Hispanic Catholics.