Syrian state media has attributed the missile strikes to Israel, the BBC reported.
A senior Syrian official threatened a military response to an alleged Israeli strike on a Hezbollah-operated weapons hub near the Damascus airport on Thursday.
Syrian state TV quoted a military source saying rockets fired from Israeli territory targeted a military area in the south-western part of the airport which caused explosions.
Syrian President Bashar al-Assad is backed in his six-year-old civil war by Russia, Iran and regional Shi'ite militias.
Rami Abdel Rahman, head of the Observatory, said the blast could be heard throughout the Syrian capitol and woke up many residents at around 3:20 AM.
Israel and Hezbollah fought a devastating 34-day war in 2006 which killed 1,200 people in Lebanon, mainly civilians, and 160 Israelis, mostly soldiers.
In Israel, Minister of Intelligence and Transportation Israel Katz declined to say whether his country carried out the strike.
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Israel's Patriot anti-aircraft missile system shot down an aerial target over the Israeli-occupied Golan Heights on Thursday, the Israeli military said.
Air strikes, said to have been carried out by Israel, have hit sites in Syria on numerous occasions, reportedly targeting weapons shipments for Hezbollah.
In an interview with Israel's Army Radio, Israeli Intelligence Minister Yisrael Katz responded to the reports.
"Every time we receive intelligence information on plans to transfer advanced weaponry to Hezbollah, we will act", the minister added. In practice, however, Hezbollah forces in Syria are focusing primarily on fighting against ISIS, which has led Syria to complain that the Israeli strikes are being done to assist ISIS. Iran is also an ally of the Syrian government.
As well as weapons, hundreds of Shi'ite militia fighters from Iraq and Iran have been flown to Damascus worldwide airport.
On Wednesday, a high-ranking Israeli military officer briefed reporters that approximately 100 missiles intended for Hezbollah had been destroyed in the raid.
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