The military described the shellfire into the Israeli-held territory as errant fire and called it an "unacceptable breach" of sovereignty.
Two hours after the projectiles landed, the IDF announced that "IAF [Israel Air Force] aircraft targeted the position from which the launches originated".
Israel has tried to stay out of the six-year civil war in Syria and refrained from taking sides, but has responded to spillover fire on numerous occasions. No one is reported to have been wounded as a result of the projectile fire. It has responded in the past with limited strikes when fire has spilled into Israel.
"The [Syrian] army repelled a massive al-Nusra Front attack on the city of Baath in the Quneitra province [bordering the Golan Heights]".
"With the IDF action today [24 June], we are making our policy clear again".
Israel's military has asked Israelis to keep their distance from the Syrian border area. Backpackers and hikers were also evacuated from he area.
The Israeli Air Force also targeted two Syrian regime tanks in the northern part of the Golan, the spokesman said, adding the projectiles did not cause any casualties.
On Sunday, Netanyahu warned Iran against setting up a military presence in Syria and allegedly arming Hezbollah.
It said that "more than 10" rockets had fired from Syria earlier.
Damascus says Israel and its Western and regional allies are aiding Takfiri terrorist groups operating inside the Arab country, while the Tel Aviv regime's military carries out sporadic strikes against Syrian government forces.
The warring sides involved in the conflict are numerous. The cooperation began when the Israelis began assisting Syrian fighters, including alleged "Islamist extremists", through medical care at Israeli hospitals, in a relationship that soon led to direct funding for fighters for salaries, ammunition and weapons.