He added that he wishes "wisdom and prudence prevail, in order to avoid adding new elements of tension to a global panorama that is already convulsed and marked by so many and cruel conflicts".
U.S. President Donald Trump has made clear his intention to recognize Jerusalem as the capital of Israel and move the embassy there from its current position in Tel Aviv.
His intervention comes ahead of the expected announcement that the United States will recognise Jerusalem as Israel's capital.
At the meeting, the pope said dialogue between all parties would come only through "recognising the rights of all people", noting that the Holy Land was the "land par excellence of dialogue between God and mankind".
Pope Francis, who had returned to the Vatican late the night before after a six-day trip to Myanmar and Bangladesh, also used his midday address as an opportunity to thank everyone who had prayed for the trip's success and everyone who had a hand in organizing it.
Palestinians and Arab leaders across the region have criticized President Trump's decision, which includes a plan to move the USA embassy from Tel Aviv to Jerusalem.
The decision could potentially dismantle 22 years of US foreign policy in the Middle East and would likely enrage Muslims who view Jerusalem as the potential capital of the Palestinian state.
The Holy See recognised the Palestinian state in 2015.
In 2012, the Vatican called for "an internationally guaranteed special statute" for Jerusalem, aimed at "safeguarding the freedom of religion and of conscience, the identity and sacred character of Jerusalem as a Holy City, (and) respect for, and freedom of, access to its holy places".
The Vatican and Israel established full diplomatic relations in 1994.
The position of the United Nations on the Jerusalem issue is that East Jerusalem is occupied Palestinian territory and that the city should eventually become the capital of the two states of Israel and Palestine.
"I wanted, also in this case, to express the closeness of Christ and of the Church to a people that has suffered due to conflict and repression and which now is slowly walking toward a new condition of freedom and peace", he said.