Tensions flare as Israel hits 'Hizballah targets' in Syria
It was the most serious incident between the two countries, which remain technically at war, since civil war broke out in Syria in March 2011.
"Overnight... aircraft targeted several targets in Syria," an Israeli army statement said.
"Several anti-aircraft missiles were launched from Syria following the mission and (army) aerial defence systems intercepted one of the missiles."
None of the missiles hit their targets, the army added.
Both Israeli and foreign media have reported Israeli airstrikes inside Syria targeting arms convoys allegedly headed for Lebanese militant group Hizballah, which fought a devastating 2006 war with Israel and is now fighting alongside the Damascus regime.
But normally Israel makes no official comment on such operations.
The missile fire prompted air raid sirens to go off in the Jordan Valley during the night, the Israeli army said.
The missile was intercepted north of Jerusalem by Israel's Arrow air defence system, Israeli media reported.
A Jordanian civil defense source quoted by Reuters said a projectile had landed in a village on the outskirts of the northern Jordanian city of Irbid, about 20 kilometers (12 miles) from the Syrian and Israeli borders, causing light damage.
The Syrian army said it had shot down an Israeli jet during the raids. Israel denied this, saying that all its aircraft had returned unscathed.
In 1981 Israel annexed a large part of the Golan Heights which it seized from Syria in the 1967 Six Day War.
The annexation is still not recognised by the international community, which considers the territory Syrian.