Otari had a warning for Israel that Damascus is ready to fight if attack.
"Syria is capable of defending itself if it's exposed to any aggression, and I am sure that the Arab masses would stand by it if the Zionist enemy contemplated a new adventure," he told a news conference with his Jordanian counterpart.
Syria protested the overflight, as well as the Israeli incursion in Gaza, in a letter to the UN Security Council on Thursday that called on the world to rein in Israel, the official Syrian Arab News Agency reported.
"At a time when Israel is seeking to aggravate the situation in all parts of the region, there came its provocation against Syria," the letter said.
Wednesday's flyover was the second time Israel has buzzed Assad's summer palace. In August 2003, warplanes reportedly flew so low that windows in the palace shattered. At the time, Israel said the flyover was aimed at pressuring Assad to dismantle Palestinian militant groups based in his country. In October 2003, an Israeli warplane bombed an Islamic Jihad training base near the capital Damascus in the first attack on Syrian soil in more than two decades.
The airstrike followed a suicide bombing by Islamic Jihad that killed 19 Israelis in a restaurant.
Osama Hamdan, Hamas' Lebanon representative who is close to Hamas' Damascus-based political leader Khaled Mashaal, said Syria and his group would not be intimidated by the overflights.
"Experience has shown that this kind of pressure will not be a useful means with the Syrians or with us," Hamdan said.
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