Despite their differences, the president presented the pope with the Presidential Medal of Freedom, the highest U.S. award for a civilian, following a private meeting with the pontiff.
Before receiving the award, Pope John Paul and President Bush made public statements.
"It is the evident desire of everyone that this situation now be normalized as quickly as possible with the active participation of the international community and, in particular, the United Nations organization, in order to ensure a speedy return of Iraq's sovereignty, in conditions of security for all its people," the pope said.
The president presented the pope with the award, calling him "a devoted servant of God."
"We appreciate the strong symbol of freedom that you have stood for and we recognize the power of freedom to change societies and to change the world," President Bush told the pope.
Mr. Bush is on a three-day trip to Italy and France to seek international support for rebuilding Iraq and to commemorate the 60th anniversaries of the liberation of Rome on June 4 and the D-Day invasion of Normandy on June 6.
Ahead of the visit, Italy's prime minister, Silvio Berlusconi, who has supported the U.S. coalition in Iraq, worried about violent protestors. He asked demonstrators to show "maturity and understanding of history."
Thousands of police were deployed to monitor demonstrations that included tens of thousands of Italians calling for an end to the occupation of Iraq.
Many Italians did not support Berlusconi's decision to send Italian troops to Iraq, which the prime minister has vowed to keep there despite the opposition.
During his visit, President Bush laid a wreath at Fosee Aredeatine, where Nazis killed 335 men and boys during World War II, according to the Associated Press.
Originally, President Bush was supposed to lay a wreath at Italy's Tomb of the Unknown Soldier, but plans changed for security reasons.
On Saturday, the president will meet with French President Jacques Chirac before the commemoration on Sunday of the 60th anniversary of the D-Day invasion.
The president is also set to meet with German Chancellor Gerhard Schroeder while in France. Both Chirac and Schroeder opposed the war in Iraq. Despite those differences, U.S. officials said the meetings would focus on the future of the war-torn nation.
"Whatever differences we had in the past, that a free and prosperous and stable Iraq is a linchpin and a key to a stable Middle East is understood," said national security adviser Condoleezza Rice. She added, "People are looking for ways that they can help get that done."
As diplomats continue to hammer out a new U.N. Security Council resolution for the Iraqi government transition, U.S. officials have reached out to nations that opposed the war for support, including France, Russia and China.