Shoigu said the new system will "significantly increase" the Syrian army's combat capabilities.
"The S-300 was a deal that had been signed with Syria in 2013, but Israel put its foot down on negotiation with Russian Federation and Russia decided that it was going to hold off delivering these units", he said.
"We are convinced that these measures will calm down some hotheads and keep them from careless actions which pose a threat to our troops", Mr Shoigu said.
Last week, a Russian Il-20 plane with 15 people on board was shot down by a Syrian anti-aircraft missile over the Mediterranean Sea off the coast of Latakia governorate.
"(Russia will) transfer the modern S-300 air defense system to the Syrian armed forces within two weeks".
Russia's military Sunday blamed "misleading" information from the Israeli airforce for the downing of one of its planes in Syria last week, and denounced the "adventurism" of Israeli pilots. Now "the Syrian air defense will be able to identify Russian planes", he added.
The Defense Ministry released detailed computer simulations over the weekend that it said showed that Israeli planes used the Russian reconnaissance aircraft as cover.
A dispute between Israel and Russian Federation could restrict Israel's ability to mount air raids inside Syria on what it considers the greatest threat to its security from the Syria conflict: the build-up of Iranian forces or Iranian-backed Hezbollah fighters.
The "adventurism" of the Israeli military could have endangered civilian planes which use the same airspace to land at the nearby Hmeimim aerodrome, the officer said. Liability falls on Israel, the ministry said, because warning of the strike came just one minute in advance.
A Russian plane was accidentally shot down by Syria as Israeli jets were attacking Assad regime targets in the war-torn country last week.
"According to information of our military experts, the reason [behind the downing] was premeditated actions by Israeli pilots which certainly can not but harm our relations", Kremlin spokesman Dmitry Peskov was quoted as telling journalists.
The Kremlin said Russia's decision was not targeted against anyone and only serves to protect Russian troops in Syria.
"Russia in this case is acting in its interests only, these actions are not directed against third countries, but towards defending our own military", he said.
It was the deadliest known case of friendly fire between Syria and key backer Russian Federation since Moscow's game-changing 2015 military intervention.
"We're confident that these measures will cool "hot heads" and prevent thoughtless moves that threaten our servicemen", he said. It is possible that these aircraft delivered of the S-300 air defense systems to Syria.