The head of the Observatory, Rami Abdel Rahman, told dpa the strikes targeted posts and arms depots for the Iranian Revolutionary Guard in the southern countryside of Damascus.
He said the attack was close to the Shiite shrine of Seyyeda Zeinab on the southern outskirts of Damascus. 
The state-run SANA news agency reported that Syrian army air defences intercepted "hostile missiles" in a region in the countryside of Damascus, without mentioning casualties. 
It said the "missiles were coming from the occupied lands," referring to Israel.
"The Israeli enemy yesterday launched a missile attack that targeted Damascus and its surroundings," Syrian Foreign Minister Walid al-Moallem was quoted by SANA as saying, after talks with his counterpart Sergey Lavrov in Moscow.
A Lebanese army source said the Israeli planes used Lebanese airspace to fire at targets inside Syria.
"This blatant assault is condemned. I call on the international community to intervene to prevent these repeated attacks on Lebanese sovereignty," Lebanese caretaker Defence Minister Elia Bou Saab said on his Twitter account.
Israel did not confirm the missile strikes. An army spokesman said "we are not commenting on reports in foreign media."
Israel has said previously that its rocket attacks and airstrikes on Syria are aimed at preventing Iran from building up its military influence in the region.
Iran and the Lebanese Shiite Hezbollah movement are the main allies of Syrian President Bashar al-Assad.
In north-east Syria, a blast rocked the city of Suluk, which is held by Turkish-backed rebels, killing five people and wounding 21 others, the Observatory said. 
The injured included women and children, the war monitor said, adding that heavy material damage was inflicted as the result of the blast.
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