Mottaki, who said he had brought a letter from President Mahmoud Ahmadinejad, said he and Assad had "agreed on the need to bring an end to the occupation of Iraq with a view to achieving stability," state news agency Sana reported.
He added the message contains regional issues as well as mutual ties, the IRNA news agency reported.
He said they stressed the importance of the "constructive participation of all Iraqis in self-determination" in their country and the "need to support the government of that country so that it can assume its responsibilities."
Both Syria and Iran have been accused by the United States of contributing to instability in Iraq.
IRNA reported that Mottaki, who arrived in Damascus Saturday evening on an official invitation of Syrian Foreign Minister Walid al-Moalem, said he would also hold talks with Syrian officials concerning bilateral relations and the latest regional developments in Iraq, Palestine and Lebanon.
Mottaki noted that the officials of the two countries in different levels, with the aim of promotion of bilateral cooperation between Iran and Syria consult with each other once in a while.
Dudi Cohen contributed to the report