Defence Minister Binyamin Ben Eliezer said the guerrillas could not have launched recent attacks on Israel without the knowledge and approval of Syria, which has a large military contingent in the country.
Hezbollah fighters are reported to have fired mortars and rockets on at least three Israeli positions in the disputed Shebaa Farms border area on Saturday.
"We do not want to open a new front, we do not want an escalation but this operation could not have taken place without the knowledge and authorisation of Syria," Mr Ben Eliezer said.
Witnesses described heavy smoke rising from one Israeli military post after the Hezbollah attacks.
Israeli jets responded by firing several air-to-surface missiles and Israeli artillery reportedly shelled the outskirts of Hasbaya, a town on the Lebanese side of the border.
There were no reports of casualties.
Flashpoint
It was the first Israeli raid on southern Lebanon since late January.
A Hezbollah statement said the guerrilla attacks were part of the organisation's campaign to "liberate" the area from Israeli control.
An Israeli army spokesman said it was a deliberate attempt to escalate the conflict.
"Hezbollah wishes in a crude and violent fashion to heat up the area and provoke Israel," said Lieutenant Colonel Olivier Rafowicz.
The Shebaa Farms have been a flashpoint since Israel pulled out of Lebanon in May 2000.
Israel seized the farms in 1967 from Syria, but Lebanon claims the area as its territory.