The Syrians said it was Arafat who made what was the first such call in years to a top Syrian official. But Palestinians hinted it was the other way round.
The phone call was significant, particularly since relations between the Palestinians and the Syrians had been chilly and the two sides have had little high-level contacts over the years.
Syria's official news agency said Arafat called to express his gratitude for Syrian support after Israel's security cabinet decided in principle to expel the Palestinian leader.
Arafat was quoted as expressing his gratitude for Syrian President Bashar al-Asad's "daring and constant stands in support of the Palestinian people's rights."
The Palestinians, including top Arafat aide Nabil Abu Rdeneh, however insisted it was the Syrian minister who called to extend support to the Palestinian leader.
The phone call was significant, particularly since relations between the Palestinians and the Syrians have been chilly.
Rdeneh said it was the first call Syria's leadership has made in recent memory.
"This is an important phone call and Faruk al-Shara expressed Syrian President's support," he said.
"This is a very important and strong message from the Syrians," he added.
Relations between the Palestinians and the Syrians soured when Arafat fell out with Syria's late president, Hafez Asad.
There have been no-high level contacts between the Syrians and Arafat since the Palestinian leader planned to visit Damascus in September 2001.
That trip was abruptly cancelled at the last minute, with each side blaming the other for the change of plans.