A decree was issued by President Dmitry Medvedev prohibiting the sale, which had been in the pipeline for years.
Earlier, Gen Nikolai Makarov, head of Russia's general staff, confirmed that the missiles were "definitely" subject to the sanctions introduced in June.
At that time, Russia's foreign minister said the S-300 deal was not affected.
Possession of S-300 systems would enhance Iran's defence of its nuclear facilities against attack from the air.
Mr Medvedev's decree, published on Kremlin website, lists the S-300 among military items which must not be exported to Iran under the fourth round of sanctions imposed by the UN Security Council on Iran over its nuclear programme.
However, shortly afterwards, Prime Minister Vladimir Putin was quoted by French media as saying the sale had been suspended.
There has long been speculation that Israel may attempt to bomb Iranian facilities to prevent Iran acquiring nuclear weapons.
Iran denies seeking nuclear weapons, insisting that its programme is purely civilian.
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