Musharraf, who is on a three-day state visit to Italy, met the Pope at the Vatican Thursday after a lengthy call on Italian Prime Minister Silvio Berlusconi.
"In these times of turmoil and violence," John Paul told Musharraf, "I encourage you and your fellow citizens to continue to foster a spirit of dialogue and tolerance in your region."
Invoking "the abundant blessings of the Almighty God" on the Pakistani people, he said "It is only by acknowledging the need for mutual understanding among peoples, through a frank and open exchange of ideas, that the world can obtain justice and peace."
Earlier, Berlusconi and Musharraf released a joint statement firmly opposing any expansion in the number of permanent members on the United Nations Security Council.
The Council currently has five permanent seats -- Britain, China, France, Russia and the United States -- and 10 seats which rotate between UN nations.
While Italy is alarmed at Germany's bid for a seat on the Council, Pakistan fears India's attempts to get on board. Other contenders include Japan and Brazil.