The original deal, signed in Damascus in January, set out the terms under which Russia can use its Hmeymim air base in Latakia Province, which it has used to carry out air strikes against forces opposing President Bashar al-Assad.
Mr Putin approved the agreement after the two chambers of the Russian parliament backed it earlier this month, according to the government's official information portal.
The document says Russian forces will be deployed at the Hmeymim base for 49 years with the option of extending that arrangement for 25-year periods.
The base has been at the heart of Moscow's military foray since it intervened in the conflict in September 2015, helping turn the tide in favour of Assad, one of Russia's closest Middle East allies.
Last week, the Syrian president visited the airfield to inspect weapons, personnel and armoured vehicles.
He was pictured sitting in the cockpit of a Russian Sukhoi SU-35.
Additional reporting by Reuters
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