A decree signed by Putin removes a ban on "the shipment from Russia to Iran" of the S-300 missiles, the Kremlin said in a statement.
Moscow blocked deliveries of the surface-to-air missiles to Tehran in 2010 after the United Nations slapped sanctions on Iran over its nuclear programme barring hi-tech weapons sales.
Iran then filed a USD 4-billion suit against Moscow at an arbitration court in Geneva.
The decision to lift the delivery freeze comes after Tehran and international powers including Russia made a major breakthrough this month by agreeing an outline deal aimed at curbing Iran's nuclear programme.
More From This Section
Global powers must resolve a series of difficult technical issues by a June 30 deadline for a final deal, including the steps for lifting global sanctions imposed on Iran, and lingering questions over the possible military dimensions of its nuclear programme.
Iran's Supreme leader Ayatollah Ali Khamenei, who will have the final say on any deal, has plunged the accord into doubt suggesting that "nothing is binding" while President Hassan Rouhani demanded that sanctions be immediately lifted when any deal is signed.
Despite the dispute over the S-300 missiles, Moscow and Iran have remained on good terms, with Russia agreeing to build new nuclear reactors for Tehran and both sides supporting President Bashar al-Assad in Syria.