Syrian rebels led by Shaaraa captured Damascus in December and ousted longtime president and Moscow ally Bashar al-Assad, who has now taken refuge in Russia.
Moscow has officially recognized the new Syrian government.
The Kremlin has released a video of the first minutes of Putin and Shaara's meeting.
Putin said that Moscow has always been"guided by the interests of the Syrian people" in its relations with Damascus, and recalled that these relations have always been friendly.
Sharaa, in turn, assured that the Syrian authorities would abide by all agreements previously reached with Russia.
Kremlin spokesman Dmitry Peskov said before the meeting that the leaders would also talk about Russian military bases in Syria, which were established during the Assad regime.
Russia's military presence in the country has been reduced, but bases in Hmeimim and the port of Tartus remain.
Reuters and several Arab media outlets reported before the visit that Shaaraa could formally request Assad's extradition during talks in Moscow.
Russia intervened in the Syrian civil war on Assad's side in 2015.