Vatican spokesman Fr. Frederico Lombardi called the invitation a "surprise" and "an initiative of the Pope."
The Mass for at least 9,000 Palestinians and pilgrims in the Holy Land erupted in applause when during the sign of peace Pope Francis came around the altar and embraced President Abbas, leader of the Fatah party and head of the Palestinian Authority.
The gesture of solidarity and respect to the Palestinian people echoed an earlier moment when Francis was passing by the separation wall that runs through Bethlehem, separating the Palestinian from settler communities all around it. The Pope stopped his vehicle, got out and prayed silently for three or four minutes before touching his forehead to the wall.
"It was not a blessing. It was a sign of participation… He has demonstrated his awareness," said Lombardi.
By praying silently the Pope was not taking sides in the bitter dispute between Palestinians and Israelis, said Lombardi.
"It was without a word or any other manifestation of polemic," said Lombardi.
Francis message to Abbas and Perez at the end of the Mass was they have a duty on behalf of their people to strive for peace.
"We have the duty to become instruments and artisans of peace," he said. The Pope hammered home that life without peace is intolerable.
"Living without peace is constant torment," he said.
After those words, with a final blessing, Manger Square erupted into shouts, screams and applause with flags waving and banners raised high.