A Reuters reporter heard at least four strikes as drones could be heard over the predominantly Druze city of Sweida on Tuesday and saw a damaged tank being towed away.
Dozens of people have been killed in fighting in the region since Sunday.
The upsurge in violence underlines the challenges facing interim President Ahmed al-Sharaa who has struggled to assert control over the area near the Israeli border since toppling Bashar al-Assad in December.
While Sharaa has been buoyed by rapidly improving ties with US President Donald Trump's administration, the violence has highlighted lingering sectarian tensions and distrust among minority groups towards his Islamist-led government - distrust that was deepened by mass killings of Alawites in March.
Israel, which has struck Syria several times in the name of protecting the Druze, carried out its latest attacks after influential Druze Sheikh Hikmat al-Hajri issued a statement accusing government troops of breaching a ceasefire and urging fighters to confront what he described as a barbaric attack.
After al-Hajiri appeared in a recorded statement, Syrian Defence Minister Murhaf Abu Qasra declared that a complete ceasefire was in place, and saying government forces would only open fire if fired upon.
Abu Qasra also said military police had been ordered to deploy in Sweida to "control military behaviour and hold violators accountable", the state news agency SANA reported.
The Druze are a minority group whose faith is an offshoot of Islam and has followers in Israel, Syria and Lebanon.
Israeli Prime Minister Benjamin Netanyahu and Defence Minister Israel Katz said they had ordered Israel's military to strike "regime forces" and weaponry brought to Sweida to be used against the Druze.
In a statement, they said the deployment of government forces was in violation of a demilitarisation policy that had called on Damascus to refrain from bringing forces and weapons into southern Syria that pose a threat to Israel.
"Israel is committed to preventing harm to the Druze in Syria due to the deep brotherhood alliance with our Druze citizens in Israel," they said.
"We are acting to prevent the Syrian regime from harming them and to ensure the demilitarisation of the area adjacent to our border with Syria."
The latest violence began on Sunday with fighting between armed Druze groups and Bedouin fighters in Sweida province, which displaced thousands of people.
The Druze spiritual leadership said in a statement on Tuesday morning that it would allow Syrian forces to enter Sweida city to stop the bloodshed, calling on armed groups to surrender their weapons and co-operate with incoming troops.
But hours later, al-Hajri, a vocal opponent of the new Syrian leadership, said the statement had been "imposed" on them by Damascus and Syrian troops had breached the arrangement by continuing to fire on residents.
"We are being subject to a total war of extermination," he said in a recorded video statement.
Convoys of Syrian army tanks, trucks and motorcycles entered parts of Sweida city by mid-morning and were continuing to fire on neighbourhoods there, the Reuters reporter in Sweida said.
On Monday, Israel's military said it had carried out several strikes on tanks approaching Sweida "to prevent their arrival to the area" because they could pose a threat to Israel.
