The Syrian Observatory for Human Rights claimed the attack killed six people - four regime soldiers and two Iran-backed fighters.
The missiles struck warehouses and sites linked to Iran-backed militias.
The strikes also caused material damage near the capital, Sana news agency quoted a military source as saying.
Israel regularly strikes Iran-linked sites in neighbouring Syria, including munition facilities near the capital.
Damascus shot down several missiles during the attack, it added, while an AFP correspondent reported hearing explosions near the capital.
Israel rarely publicly acknowledges such operations but has repeatedly warned it would act against growing Iranian influence in the region.
Israel has struck Syria 22 times this year, SOHR said, killing 59 people.
It said 24 of the dead are regime soldiers, while 22 were foreign nationals, part of Iran-affiliated militias.
Six members of Iran's Islamic Revolutionary Guard Corps and two civilians have also been killed in Israeli strikes, according to the human rights monitor.
On July 19, Israeli air strikes near Damascus killed three pro-government fighters and wounded four others, a war monitor said at the time.
A wave of Israeli air strikes were reported in Homs earlier in July.
An Israeli military spokesman said warplanes targeted a Syrian air defence battery from which an anti-aircraft missile was launched towards Israel.
A strike in May also forced Aleppo airport to close.
Israel's Defence Minister Yoav Gallant said Israeli strikes in Syria have doubled under the new government.
They aim to damage Iran's intelligence capabilities and prevent its Islamic Revolutionary Guard Corps from becoming established near the border with Israel, Mr Gallant told a security conference in May.
Damascus has previously admitted to its soldiers being killed in Israeli strikes.
One soldier was among five people killed in a missile attack on central Damascus in February, while an army colonel was killed in another strike in February.
Tehran's influence has grown in Syria since the conflict started in Syria in 2011.
Iran-linked groups, including Lebanese Hezbollah, have a significant presence in different parts of the country, including areas around the capital Damascus.
In April, the former head of Israel's National Security Council Maj Gen Yaakov Amidror said the country must "prepare for war” with Iran as it continues to grow its nuclear programme, and said it may have to strike its enemy "without American support”.
It was one of several warnings made by Israeli officials against Iran in recent months.
Mr Gallant warned that Iran's growing nuclear enrichment could "ignite the region”.
Israel announced last month that it had shut down a major cryptocurrency network funding Iran-linked groups.
The operation – the first of its kind – targeted digital wallets linked to the Islamic Revolutionary Guard Corp's elite Quds force and Hezbollah, according to Mr Gallant.