The attack was repelled by the Syrian Air Defence and most of the missiles were shot down, while a warehouse near Damascus International Airport was damaged by the strikes.
Confirming a Friday night sortie in Syria, Netanyahu said Israel's air force had "struck Iran's warehouses, containing Iranian arms, in Damascus worldwide airport".
Netanyahu also cited an Israeli search-and-dismantle mission against suspected Hezbollah attack tunnels along the border with Lebanon that was launched in December and deemed completed on Sunday. "The accumulation of recent attacks proves that we are determined more than ever to take action against Iran in Syria, just as we promised", he said as quoted by his office.
Only recently has it begun to speak publicly about thwarting the weapons smuggling from Iran through Styria into Lebanon.
Eisenkot, who will step down on Tuesday, will be replaced by Maj. "During this time we worked together against varied threats in order to build up Israel's security", Netanyahu said. Israel's outgoing military chief, Lt. Gen. Gadi Eisenkot, did so over the weekend in various interviews.
Netanyahu, visiting the northern border later on Sunday, put the number at "between 1,000 and 2,000" Hezbollah fighters.More news: Graham says Trump isn't giving in on border wall
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The final tunnel was the largest one discovered so far, running hundreds of metres from under a Lebanese home and deep into Israeli territory, military spokesman Lt Col Jonathan Conricus said.
"We have achieved the goal that we set out to achieve", he said.
Hezbollah has not commented on the tunnels, the existence of several of which has been confirmed by Unifil peacekeepers.
Israel and the United Nations say the tunnels violate a ceasefire resolution made after a 2006 war between Israel and Hezbollah.
Israel has long called for a crackdown on the Iran-backed Hezbollah, a heavily armed mini-army that is believed to possess an arsenal of some 150,000 rockets that can reach almost all of Israel. But with that war winding down, Israeli security officials fear Hezbollah is refocusing its attention on Israel.