Rai, whose church has 900,000 members in Lebanon, a quarter of the country's population, is on the first visit to Syria by a Maronite Patriarch since the independence of neighboring Lebanon in 1943.
His visit comes at a time when Christians in the region feel under threat from the rise of political Islam.
Few Christians have supported the revolt against Syrian President Bashar Assad, fearful for their future if the country's majority Sunni Muslims choose an Islamist leadership to replace decades of ruthless but secular Assad family rule.
"(I pray) that the consciences of local, regional and international leaders are inspired to put an immediate end to the war in dear Syria ... and bring peace through dialogue," he told dozens of worshipers inside the church.
Inspired by protests in some Arab countries which toppled leaders of Egypt, Tunisia and Libya, many Syrians took to the streets in 2011 calling for more freedoms. But the peaceful protests turned into war.
Lebanon's Maronite leaders have had tense relations with Syria and led calls for an end to its military presence in Lebanon in 2005. But since the civil war flared, Christians have been uneasy about supporting rebels against Assad's secular Baathists who ensured freedom of belief for minority faiths.
Rai himself has criticized the Arab Spring and said that violence and bloodshed is turning it into winter. He has always been careful not to be seen supporting either side in the Syrian conflict but has adopted a position close to Assad's by saying reforms should not be imposed from outside.'God protect you'
Clashes between government forces and rebels continued on Sunday across Syria, including in the provinces of Aleppo and Idlib and on the edge of Damascus, close to the heart of the capital, where fighting has raged for four days.
Rai, 72, said he was saddened to see people fleeing the capital as his convoy was driving into Damascus.
Walking towards the altar to say mass, he blessed visibly emotional worshipers with a cross and repeatedly told them: "God protect you, God be with you."
Divisions in the opposition and among the international powers over Syria have deprived Syria's rebels of desperately needed arms to confront Assad's heavily armed forces.
Minority groups fear an Islamist takeover and many Christians, Shiites and Kurds are reluctant to support an armed revolt that included several Sunni extremist rebel units.
Across the Arab world, Christians feel like a species facing extinction, threatened by Islamists who now hold power in Egypt and Tunisia. Christians make up about 5 percent of the Middle Eastern population, down from 20 percent a century ago.
BEIRUT (Reuters) -- The head of Lebanon's Maronite Catholic church, Patriarch Beshara al-Rai, prayed in an old Damascus church on Saturday for an end to Syria's civil war.