The encounter came at the end of today's audience which had followed a Mass of thanksgiving for Sunday's canonization.
The meeting with the Pope was the first official event of the patriarch's visit to Rome. He is repaying a visit made by the Holy Father to Rumania in 1999, the first papal visit to Orthodox lands.
During the Romanian's visit, the two religious leaders will sign a joint declaration, which should be another step toward full unity between these two Churches, separated since 1054.
"Beatitude and dear brother: You are making this visit encouraged by my same sentiments and same expectations," John Paul II said in his address to the patriarch. "To meet next to the tomb of the holy Apostles Peter and Paul is a sign of our common will to overcome the obstacles that still impede the re-establishment of full communion between us."
"The present visit is also an act of purification of our memories of division, of often fiery confrontations, of actions and words that have led to painful separations," the Pope said.
"Despite everything, the future is not a dark and unknown tunnel," he continued. "The latter is already illuminated by the grace of God; on it the vivifying light of the Spirit already throws a consoling reflection.
"This certainty not only prevails over every human discouragement, over exhaustion that sometimes halts our steps, but convinces us above all that nothing is impossible for God and that, therefore, if we are worthy, he will also grant us the gift of full unity."
The Romanian's visit ends next Sunday, the day the Pope will preside over the eucharistic liturgy in the presence of the patriarch in St. Peter's Basilica. John Paul II and the patriarch will share the Liturgy of the Word, pray together, profess the faith in the Romanian language, and separate at the moment of the Eucharistic Prayer.
"May these days be able to nourish our dialogue, our experiences, make us more aware of what unites us in our common roots of faith, of our liturgical heritage of the saints and witnesses which we have in common," the Pope concluded in his welcome address. "May the Lord make us feel once again the beauty and sweetness of invoking him together."