State media did not disclose any details of the previously unannounced visit by Sergei Shoigu, who said he was sent to the Syrian capital by Russian President Vladimir Putin.
Shoigu also visited the Hemeimeem air base in the province of Lattakia, where he talked with pilots and inspected the S-400 air defense missile systems protecting the base.
Russia's military intervention in Syria in September helped to turn the tide of war in Assad's favor after months of gains in western Syria by rebel fighters, who were aided by foreign military supplies including US-made anti-tank missiles.
Russia, which has been intensively bombing opposition-held areas in Syria since the intervention, is blamed by the opposition and rights activists for causing hundreds of civilian deaths and targeting hospitals, schools and infrastructure in what they say are indiscriminate attacks.
Washington and some other Western countries that have called on Assad to step down accuse Russia of focusing mostly on strikes against the moderate so-called Free Syrian Army (FSA) and less on attacking hardline Islamic State militants.
A US- and Russian- brokered cease-fire that began on February 27 has helped reduce hostilities, but fierce fighting has continued in many areas. The Islamic State group and the al-Qaeda branch in Syria, the Nusra Front, have been excluded from the truce.