Israel shot down what it identified only as "a target" over the occupied Golan Heights on Thursday, hours after the Assad regime accused it of hitting a military position near Damascus airport.
"The Patriot Aerial Defence System intercepted a target above the Golan Heights," the official Israeli army Twitter account said, without elaborating.
A military spokeswoman refused to comment on Israeli media reports that the object was a drone.
The regime's news agency SANA said earlier that several Israeli missiles hit near Damascus airport at dawn.
Israel has not confirmed or denied the reported Damascus attack.
But Intelligence Minister Yisrael Katz said it was consistent with Israel's policy to prevent arms transfers through to Hezbollah, while stopping short of confirming his country was behind the incident.
"We are acting to prevent the transfer of sophisticated weapons from Syria to Hezbollah in Lebanon by Iran," Katz told army radio.
"When we receive serious information about the intention to transfer weapons to Hezbollah, we will act. This incident is totally consistent with this policy."
In Moscow, the Kremlin called for restraint and the foreign ministry condemned the attack.
Kremlin spokesman Dmitry Peskov did not say if Israel had warned Moscow of the strike, saying only that their defence ministries "are in constant dialogue".
In Moscow, visiting Israeli Defence Minister Avigdor Lieberman told Russian Foreign Minister Sergei Lavrov and Defence Minister Sergei Shoigu that the Jewish state would not allow "concentration of Iranian or Hezbollah forces on the Golan border," Lieberman's office said.
Israel has conducted multiple air strikes in Syria since that country's civil war erupted in 2011, most of which it has said targeted arms convoys or warehouses of its Lebanese arch-foe Hezbollah, which is a key supporter of the Syrian regime.
Last month, it said it had carried out several strikes near the Syrian desert city of Palmyra, targeting what it said were "advanced weapons" belonging to Hezbollah.
The strikes prompted the regime to launch ground-to-air missiles, one of which was intercepted over Israeli territory in the most serious flare-up between the two neighbours since the civil war began six years ago.
Israel seized 1,200 square kilometres (460 square miles) of the Golan from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the international community.
Around 510 square kilometres of the Golan are under Syrian control.
The two countries are still technically at war, although the border remained largely quiet for decades until 2011, when the Syrian conflict broke out.