Israeli Army spokesman Lt. Col Jonathan Conricus told CNN that the unmanned aerial vehicle (UAV) or drone, had been dispatched on a specific mission inside Israel.
The Israeli military had tracked the drone from its launch inside Syria, entering Israeli air space at 4.50 a.m. local time Saturday. The drone was shot down by an Apache attack helicopter and its remains fell north of the Israeli town of Beit She'an.
The claims regarding the downed drone were "too ridiculous to be addressed," said Iranian Foreign Ministry Spokesman Bahram Qassemi.
"The government and army of Syria as an independent country have a legitimate right to defend [the country's] territorial integrity and counter any type of foreign aggression," Qassemi said on Saturday as quoted by state channel PRESS TV.
The drone was based on the Lockheed Martin RQ-170 "Sentinel," which Iran intercepted in December 2011, on what the U.S. said was a reconnaissance mission.
In May 2014, Iran said it had built a copy of the drone after reverse engineering most of the technology.
Conricus said the Israeli Defense Forces (IDF) knew from the drone's flightpath that it had a particular mission, but he wouldn't give any details, nor would he tell CNN if the drone had been armed.
He confirmed that it was the first time an Iranian drone had crossed into Israeli airspace since the start of the Syrian civil war.
"We asked for it back. We'll see how the Iranians respond," Obama told reporters in December 2011.
Iranian Gen. Hossein Salami, then-deputy commander of Iran's military, said the drone was going nowhere.
"No nation welcomes other countries' spy drones in its territory and no one sends back the spying equipment and its information back to the country of origin," he was quoted as saying by the semi-official Fars news agency.
"It makes no difference where this drone originated and which group or country sent it to invade our airspace. This was an act of invasion and belligerence," he said.
In a video posted on YouTube on Saturday, Israeli Prime Minister Benjamin Netanyahu said Israel would defend itself "from every attack and from every attempt to harm our sovereignty."
"Israel seeks peace, but we will continue to defend ourselves with determination against every attack against us, and against every attempt by Iran to establish itself militarily against us in Syria or in any other place."
"What are the Iranians trying to achieve with penetrating Israeli air space, were they testing the air defenses? Were they using the drone as a prototype? We'll never actually know what the real aim (of the launch was)," said Rodger Shanahan, a research fellow at the Lowy Institute for International Policy.
Another question for weapons experts is how much of the US drone technology Iran was able to replicate, and what that might spell for its progress in the development of other weapons, particularly ballistic missiles.
"It doesn't [appear to] have stealth tactics," Shanahan said about the Iranian drone. "It might show that all they've done is create a better drone than they did before, maybe that was the point they were trying to test out."
Israel's Air Force Chief of Staff Brig. Gen. Tomer Bar insisted Israel allowed the drone to cross into its territory in order to destroy it.
"To this day there have not been any infiltrations of Iranian UAVs and we will not tolerate any future infiltration attempts," he told CNN.
Israel followed up the strike on the drone with the dispatch of F-16s across the border to strike at the Iranian T-4 command center, which the IDF's Conricus said came under significant Syrian anti-aircraft fire. Two pilots of one fighter jet ejected. Their plane crashed in the Galilee region in northern Israel. One of the pilots was severely wounded. The other, lightly.
Twelve further targets were hit by the Israeli airforce inside Syria, said Conricus. Eight of them were Syrian targets, four were Iranian.
CNN's Mike Schwartz contributed to this report.