Israeli President Shimon Perez had accused Damascus of supplying the Islamist militant group in Lebanon with long-range scud missiles.
The Syrian government in a statement said the allegations were fabricated.
"The Syrian Arab Republic believes that Israel aims through these claims to further strain the atmosphere in the region," a statement from the Syrian foreign ministry said.
Tensions between Syria and Lebanon on one side and Israel on the other have been on the rise since a 2006 war Israeli forces waged against Hezbollah insurgents in Lebanon in 2006.
Hezbollah now is part of a unity government that also includes pro-Western Prime Minister Saad Hariri. His father Said was assassinated in 2005 and the Syrian regime was long believed to be behind it.
The government formed last November after months of deadlock following last June's general election.
Yet the country remains deeply divided and the security situation remains fragile.