Within two weeks Russian Federation will deliver to Damascus an S-300 air defense system, previously suspended on a request by Israel.
A flurry of shuttle diplomacy by Israeli officials to Russia appeared to be paying off in May, when Russian officials said just days after a visit by Netanyahu that they were not planning on selling the system to Syria.
Russian Federation indirectly blamed Israel, which had launched airstrikes against Syria in the area where the plane was operating, for the error.
"In regions near Syria over the Mediterranean Sea, there will be radio-electronic suppression of satellite navigation, on-board radar systems and communication systems of military aviation attacking objects on Syrian territory", he said.
In the phone call, initiated by Assad, Putin spoke of "additional measures to ensure the safety of Russian troops in Syria and to reinforce the country's air defense system", the Kremlin said in a statement.
Israel regularly carries out strikes in Syria against Assad's government, its Lebanese ally Hezbollah and Iranian targets.
For its part, Israel is wary of Iran's growing influence in Syria.
The decision, he said, was approved by President Vladimir Putin.
The Kremlin has accused Israel of "premeditated actions" over the downing of a Russian plane in Syria last week, warning it will harm relations between the two countries.
"You know that Israel and the Russian Federation have quite advanced relations", Kremlin spokesman Dmitry Peskov said Monday.
Russia's defence ministry has formally blamed Israel for violating an agreement aimed at preventing clashes between the two nations over the skies of Syria that led to the downing of a Russian reconnaissance aircraft.
Arguably, the most concerning thing for Israel will be the delivery to Syria of an S-300 anti-aircraft system, which will boost Syria's capabilities to deny Israel access to its airspace.
The delivery of the missile system had been suspended in 2013 following an Israeli request, according to a statement by the Russian ministry of defence.
Russian Federation had originally agreed to sell the system to Syria in 2010, but scrapped the plan at Israel's behest.
The S-300 is a relatively modern system capable of engaging targets at the range of up to 250 km. Russian Federation laid the blame on Israel, saying Israeli fighter jets had pushed the plane into Syria's line of fire.
Russian Federation in April had hinted that it would supply the S-300 to Assad's government despite Israeli objections.
"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.
For several years, Israel and Russian Federation have maintained a special hotline to prevent their air forces from clashing in the skies over Syria.
Israel strongly disputed the assertion and vowed it will continue to act against Iranian targets in neighboring Syria.