During the meeting Pope Benedict told the visiting US President that he would like to see a "regional and negotiated" solution to Middle-East conflicts.
The Pope also spoke to Bush about the war in Iraq and the plight of Christians there, and they had an "exchange of opinions" on Latin America, the Vatican has reported.
At the start of a 30-minute private meeting in the pope's study, Benedict mentioned that Bush had just come from the G8 Summit in Heiligendamm, to which the president said: "I did, your old country, and it was successful ... a lot of different opinions, but it was good."
The meeting was conducted amid heightened security as fears of violence were raised as thousands of anti-US demonstrators gathered in Rome.
As reporters were taken out of the room, the pope asked Bush whether talks with Russian premier Vladimir Putin had been successful - a response was withheld by the US President until media representatives had left.
Bush and Pope Benedict have similar views on controversial ethical issues in opposing abortion and euthanasia. However, the two hold widely differing views on the morals of the Iraq conflict.
Prior to the meeting, Bush had said to an Italian newspaper on 1 June that he wanted to "mainly listen" to Pope Benedict. Also that he was eager to talk about changes in China and Cuba if it were so fitting.
Former US ambassador to the UN John Bolton previously told the BBC that Mr Bush would give the Pope a detailed explanation of US policy on Iraq. However, he said: "But I do think it is a question of explaining the policy and not modifying it."
On Saturday, Bush will travel on to Albania and Bulgaria.
