Pope Francis concluded by asking Karekin to bless him, to bless the Catholic Church, and "to bless this our path towards full unity."
Earlier, in his homily for the divine liturgy, Catholicos Karekin II expressed his gratitude for Pope Francis' "brotherly visit" to Armenia.
The three-day visit with "our spiritual brother, Pope Francis," he said, "reconfirmed that the Holy Church of Christ is one in the spreading of the gospel of Christ in the world."
This includes caring for creation, "standing against common problems, and in the vital mission of the salvation of man who is the crown and glory of God's creation."
Karekin II also spoke on the challenges faced today against the faith, such as secularism, the distortion of spiritual and ethical values, and the shaking of the family structure.
Temptations against faith in God occur both amid hardships and amid "times of wealth and lavishness, when they are disengaged with the concerns of those who long for daily bread and are in pain and suffering," he said.
"Faith is put to the test by extremism and other kinds of ideologies; xenophobia, addictions, passions and self-centred profits."
"The root of evil in modern life is in trying to build a world without God, to construe the laws and commandments of God which bring forward economic, political, social, environmental and other problems, that day by day deepen and threaten the natural way of life."
Catholicos Karekin concluded his homily reiterating his appreciation for Pope Francis' visit.
"We and our people will always pray for you, beloved brother, and for your efforts made towards peace and prosperity of humanity and towards the advancement of the Church of Christ," he said.
"May God give you strength, bless and keep firm our Churches in love and collaboration and may He grant us new opportunities for witness of brotherhood."
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Pope Francis' June 24-26 to Armenia was organized following the invitation of Supreme Patriarch and Catholicos of All Armenians, Karekin II, the nation's civil authorities, and the Catholic Church.