Both officials met at the Russian troops' headquarters in the Syrian capital, according to the Syrian presidency and state-run SANA news agency.
The pair watched a military demonstration by the Russian troops deployed in the country, the presidency said on Tuesday, reported Efe news.
Putin sent Orthodox Christmas wishes to the Russian troops stationed in Syria, according to the source.
Russian troops have been deployed in Syria since September 2015, fighting in favour of al-Assad.
Al-Assad, for his part, said he appreciated the role of the Russian troops in the Arab country and "the Syrian people for the sacrifices they have done," alongside the army.
During the meeting they discussed recent developments in the region and plans to eradicate terrorism in Idlib, according to the source.
The Syrian troops, with Russian support, have launched an offensive in the northwestern province of Idlib, the last opposition stronghold.
They also addressed the situation in northern Syria, where Turkey launched an offensive to establish a safe zone.
Putin and al-Assad toured the Syrian capital, where they visited the Umayyad Mosque and its John the Baptist's mausoleum, according to SANA.
This is the first surprise visit the head of state has made to Russian troops since December 2017, when Putin visited an air base in the western province of Latakia.
The visit came amid escalating tensions in the Middle East after a US strike killed Iranian general Qasem Soleimani in Baghdad.
As the head of the elite Quds Force, a branch of the Islamic Revolutionary Guards Corps, Soleimani had for years wielded his country's influence across the wider Middle East, strengthening Shia militias from Lebanon to Iraq and coming to the aid of Tehran's allies, like Bashar Al Assad in Syria.
Putin is scheduled to head next to Istanbul, where he will meet on Wednesday his Turkish counterpart Recep Tayyip Erdogan.
Both are scheduled to take part in the launch of the Turk Stream natural gas pipeline, which will supply Turkey with Russian gas through the Black Sea.
( With inputs from IANS )