The Kremlin said Putin met Muallem in his Black Sea retreat of Sochi, but provided no other details.
"The meeting was devoted to Russian-Syrian relations," the Kremlin said in a two-sentence statement.
Images distributed by Putin's office showed Muallem also meeting his Russian counterpart Sergei Lavrov.
Russian officials earlier said they intended to offer Moscow as the venue for a restart of abandoned peace talks between the regime of Syrian President Bashar al-Assad and various opposition groups.
"The issue of mending the political process will assume an important place during the visit," the Russian foreign ministry said in a statement issued ahead of the Sochi talks.
"We intend to confirm our readiness to offer the 'Moscow Platform' for conducting the corresponding contacts between the Syrian government and a broad spectrum of social and political forces in Syrian society," the Russian statement said.
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Muallem was quoted earlier this month in Lebanon's Al-Akhbar newspaper saying that he also intended to raise the issue of Russia's stalled shipment of sophisticated S-300 missiles to protect Syrian forces from possible US air strikes.
Russia -- now embroiled in a major diplomatic row with the West over Ukraine -- suspended the weapons' delivery in 2013 under pressure from Israel and the United States.
The multi-sided Syrian conflict has killed more than 195,000 people and forced millions from their homes since it began in early 2011 as an uprising against Assad's regime.
Two previous rounds of Syria peace negotiations in Geneva in June 2012 and last January ended in failure and no new meetings in Switzerland are currently being planned.
Syrian opposition leaders have paid a series of brief visits to Moscow that only highlighted stark differences between the two sides.
The fractured opposition is furious at Russia for providing Assad's forces with weapons and offering diplomatic backing for Syria at the United Nations.
Moscow in turn accuses the rebels of rejecting political dialogue and in some cases engaging in terrorism.
Damascus was an important Middle East ally of Moscow in the Soviet. Russia and Iran remain two of the most important and powerful friends of the Assad regime.