Valid for 49 years, it allows for the expansion and modernisation of the facility used by the Russian navy.
Under the deal, a maximum of 11 Russian warships including nuclear-powered vessels can be present at Tartus at any given time.
"The agreement allows the expansion of the naval facility to 24 hectares free of charge," said Deputy Defence Minister Nikolai Pankov on presenting the deal to the State Duma, Russian media reported.
During a surprise visit to Syria last week, Putin ordered a partial withdrawal of Russian troops from the war-torn country, after which the military said it had begun scaling back its deployment.
Russia intervened in the Syrian conflict on the side of the Damascus regime in September 2015.
Since then, its warships have played a prominent role backing up an aerial bombing campaign in support of leader Bashar al-Assad.
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