Jaafari told a press conference at Damascus airport that he met with the embattled president this morning and held talks with his Syrian counterpart Walid Muallem.
Syrian state television reported that the two foreign ministers discussed combatting terrorism.
According to Syria's official news agency SANA, deputy foreign minister Faisal Muqdad met Jaafari at Damascus airport.
In June 2014, Damascus announced its readiness to coordinate with Baghdad in order to face the threat posed by the Islamic State group, which has a strong presence in both countries.
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Fayyad's visit came shortly after a US-led coalition began its air strikes against IS, which controls large swathes of territory in Syria and Iraq.
Shiite militias are supporting both Iraqi forces and Syrian regime troops in attempts to retake territory from IS.
While the Syrian regime's diplomatic links have deteriorated worldwide, particularly with Gulf countries, it has maintained ties with Baghdad.