"The message that I would like to draw today is this: to achieve peace one has to be committed, leaving behind violence and weapons, committed to the conversion of people and communities, to dialogue, to the patient search for possible understandings," he said at the end of the concert.
The concert, held in the courtyard of the papal summer residence south of Rome, was attended by Italian President Giorgio Napolitano.
The orchestra, which Barenboim founded together with the late Palestinian literary scholar Edward Said, brings together young musicians from various ethnic and national backgrounds in the Middle East each summer.
The idea is to let music be the food of dialogue among Arabs and Israelis.
The orchestra played Beethoven's symphonies numbers 5 and 6 at the concert, held on the feast of Saint Benedict.
In his address, the German pope noted that he and Barenboim's parents were from the generation that lived through World War Two and the Shoah, the Hebrew word for the Nazi attempt to exterminate the Jews.
"The great symphony of peace among people is never totally complete," Benedict said.
