One of those planes, a United States-made F-16, crashed on its return from that mission, landing in an empty field near near the northern Israeli village of Harduf, and one of the pilots was injured as they ejected, the Israeli military said.
Pro-Iran Al-Mayadeen channel reported that Syria's air defense systems intercepted more than 70 percent of Israeli missile attacks on Saturday - a claim that Israel categorically denied.
The incident in and of itself is a serious event and raises questions as to whether the drone was used as bait by the Iranians to drag Israeli jets into Syria, whose air defenses were laying in wait for them.
Meanwhile, Iran's Foreign Ministry rejected as "ridiculous" reports that Israel had intercepted an Iranian drone launched from Syria, state TV reported.
"This is not the first time that we have warned you of Iran's unsafe actions that undermine the situation in our region", ambassador Danny Danon wrote in the letter. Netanyahu pointed out that he has "been warning for some time about the dangers of Iran's military entrenchment in Syria".
"We urge all parties involved to exercise restraint and to avoid any actions that could lead to an even greater complication of the situation", Russia's Foreign Ministry said in a statement.
The Israeli military declined comment. It was shot down by an Israeli attack helicopter.
According to the statement, 12 targets were attacked inside Syria, including three Syrians air defense batteries and four Iranian targets that were part of Iran's buildup in Syria.More news: No. 3 Justice Department Official Rachel Brand Will Step Down
Russian Federation has also called for restraint in Syria to avoid escalating the situation.
"This is a serious Iranian attack on Israeli territory".
Israel then launched a second bombing raid in Syria. "Israel will defend its citizens and will not tolerate any violation of its sovereignty".
The semi-official Iranian news agency Isna quoted Revolutionary Guards deputy commander Hossein Salam as saying: "We can destroy all American bases in the region".
Russian Federation views Iran as a key player in resolving the crisis in Syria, but with today's events, the message Israel passed to Tehran via Moscow was either not received or was ignored by the Islamic Republic, which is investing serious efforts in how Syria will look once the disastrous war ends.
US Secretary of State Rex Tillerson is expected to visit the region in the coming week to discuss Syria and other issues, and is scheduled to visit Jordan, Turkey, Lebanon and other countries.
Hizbollah and Israel last fought a major conflict in 2006.
The Israelis were met with heavy anti-aircraft fire and one F-16 is believed to have been struck by a surface-to-air missile.
Israel also sent a similar message to the US administration to mediate to defuse tension between Israel and Lebanon over Israel's building of a border fence between the two countries.