Israeli strikes on Syrian army targets show co-ordination with "terrorists" including al-Qaeda linked militants, the Syrian foreign ministry has said.
The strikes had led to a number of casualties and widespread damage, it reported in a letter sent to the UN.
State media said a research centre and other sites had been hit overnight. Israeli sources said weapons bound for Hezbollah in Lebanon were the target.
The strike, the second in two days, drew condemnation from the Arab League.
Syria's government refers to rebels fighting against it as "terrorists".
On Friday, Israeli aircraft hit a shipment of missiles near the Lebanon border, according to unnamed US and Israeli officials.
The BBC's Yolande Knell in Jerusalem says the latest developments are a significant escalation in Israel's involvement in the conflict.
The Syrian foreign ministry statement said three military sites had been hit - a research centre at Jamraya, a paragliding airport in the al-Dimas area of Damascus and a site in Maysaloun.
"The flagrant Israeli attack on armed forces sites in Syria underlines the co-ordination between 'Israel', terrorist groups and... the al-Nusra Front," the statement said, referring to al-Qaeda militants fighting with the rebels.
"The Israeli attack led to the fall of a number of martyrs and wounded from the ranks of Syrian citizens, and led to widespread destruction in these sites and in the civilian districts near to them."
The statement added: "This leaves no room for doubt Israel is the beneficiary, the mover and sometime the executor of the terrorist acts which Syria is witnessing and which target it as a state and people directly or through its tools inside."
The Syrian cabinet held an emergency meeting on the attacks, after which Information Minister Omran al-Zohbi read a statement at a news conference.
He said the attack made the Middle East "more dangerous" and "opens the door wide to all possibilities".
Syria had the right and the duty "to defend its people by all available means," he added.
In the latest attack, Damascus was shaken by repeated explosions coming from the north-western suburbs.
Amateur video footage and eyewitness testimony suggested rocket attacks had hit weapons dumps, triggering dramatic orange-flamed blasts.
The area houses numerous military facilities, including the Jamraya research centre, designated by Syria as a scientific research centre "in charge of raising our level of resistance and self-defence".
Damascus-based journalist Alaa Ebrahim told the BBC it was "the biggest explosion" the city had seen since the conflict began two years ago.
He said residents living near Jamraya reported feeling a "mild earthquake" just before the blast, indicating that the rockets may have hit an underground facility.
Our correspondent says the Israeli attack is a high-risk strategy, and it has drawn strong reaction from the rest of the Arab world.
The Egyptian presidency said they "violated international law and principles that will further complicate the situation".
"Despite its strong opposition to bloodshed in Syria and the Syrian army's use of weapons against its people... Egypt rejects at the same time the assault on Syria's capabilities, violation of its sovereignty, and exploitation of its internal crisis under any pretext," the presidency's statement said.
And the Arab League, which has given its Syria seat to the rebels, called on the UN Security Council to "act immediately" to end the attacks.
The Jamraya facility was also apparently hit in an Israeli air strike in January.
Israeli officials confirmed the January strike, but insisted trucks carrying missiles to Hezbollah were the target.
After the latest attack, unnamed Western intelligence sources said the target was a weapons cache heading for Lebanon.
Israel has repeatedly said it would act if it felt advanced weapons were being transferred to militant groups in the region, especially Hezbollah.
Correction (7 May 2013): The headline of this report has been amended to make clear that the claim that Israeli air strikes had been co-ordinated with the rebels was made by Syrian officials.