The attack near Hader at the frontier of the Israeli-occupied Golan Heights caused only material damages, state news agency SANA cited a military source as saying.
The military issued a statement warning that it "will not allow any violation of Israeli airspace and will act against any attempt to hurt its civilians".
The anti-aircraft alarm system went off earlier on Wednesday in the Golan Heights, which are controlled by Israel, and in the Jordan River valley.
An Israeli soldier runs to direct a M113 armored personal vehicle near the Syrian border in the Israel-annexed Golan Heights on 10 May 2018.
According to Haaretz, the drone was tracked after it went about 6 miles into Israeli territory.
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Israel has been on high alert as Syrian regime forces advance on the opposition and rebels in the vicinity of the Golan, which Israel took from Syria in the 1967 Middle East war.
In a series of posts on Twitter the Israeli army said it hit the three military posts "in response to the infiltration of the Syrian UAV into Israel".
Talks also are expected to concentrate on Israel's fight against Iranian presence in Syria. The 1974 agreement officially ended the 1973 Yom Kippur War between Israel and Syria.
Shoygu remarks coincide with visits by Israeli Prime Minister Benjamin Netanyahu, the Palestinian Authority President, Mahmoud Abbas and an adviser to Iran's Supreme Leader, Ali Akbar Velayati, to Russian Federation.
Netanyahu said he planned to discuss Syria, Iran and Israeli security needs with the Russian leader.
At least some of the missiles were thwarted by Syrian air defences, they said. Israel neither confirmed nor denied carrying out that strike.
Since mid-June, the Syrian army has conducted an operation in the south-west of the republic near the border with Israel against the terror group Jabhat al-Nusra (outlawed in Russia) and armed groups supporting it.