The Israeli army confirmed it carried out strikes on Syrian and Iranian "terror targets" near Damascus on Wednesday, in response to fire from Syria the day before.
The Israel Defence Forces, who blamed Tuesday's rockets on "an Iranian force", said it holds Damascus responsible for attacks launched from Syria into its territory.
Syria's state media earlier said Syrian anti-aircraft defences intercepted a "heavy attack" by Israeli warplanes over the capital in the early hours of Wednesday morning.
Israel has carried out frequent air and missile strikes against Iranian targets inside Syria since the country descended into civil war in 2011, but rarely comments on them.
"We just carried out wide-scale strikes of Iranian Quds Force & Syrian Armed Forces targets in Syria in response to the rockets fired at Israel by an Iranian force in Syria last night," the Israel Defence Forces tweeted.
During the attack the Syrian government's defence missile was fired "despite clear warnings to refrain from such fire", it added. As a result, a number of Syrian aerial defence batteries were destroyed.
"We hold the Syrian regime responsible for the actions that take place in Syrian territory and warn them against allowing further attacks against Israel," the army said.
"We will continue operating firmly and for as long as necessary against the Iranian entrenchment in Syria."
An AFP correspondent in Damascus heard several large explosions in the early hours of Wednesday morning.
"Our air defence confronted the heavy attack and intercepted the hostile missiles, and was able to destroy most of them before reaching their targets," Syria's SANA news agency quoted a military source as saying.
SANA added that the aggression was carried out from "Lebanese and Palestinian territories". Israel sometimes launches its attacks on Syria from planes flying over neighbouring Lebanon.
Triggered by the repression of demonstrations by President Bashar al-Assad, the Syrian conflict has been complicated by the involvement of foreign powers.
Wednesday's air raid comes a day after Israel's defences intercepted four rockets fired from Syria.
The Syrian Observatory for Human Rights said Tuesday's rockets were fired from positions around the capital held by groups loyal to the Damascus government.
The flare-up follows a major escalation in and around Gaza last week when Israel carried out the targeted killing of a top commander of Palestinian militant group Islamic Jihad, which is allied with Damascus.
The killing was accompanied by a second strike, unconfirmed by Israel, on an Islamic Jihad leader in Damascus that killed his son and another person.
The hundreds of strikes carried out by Israel in Syria have mostly been against Iranian targets or positions of Iran's Lebanese ally, Shiite militant group Hezbollah.
Both are sworn enemies of the Jewish state and both have backed the Syrian president's forces with advisers or fighters.
The war in Syria has killed more than 370,000 people and displaced millions.