The surprise offensive targeted pro-government troops at positions on the main road linking the capital of Damascus to Aleppo, UK-based war monitor The Syrian Observatory for Human Rights said on Thursday.
Several Shia-majority settlements were also attacked and the village of Aqareb al-Safi captured, raising fears that the Sunni militants may massacre its residents.
The extremists have killed Muslims they regard as heretics after capturing territory on countless occasions across Syria and Iraq.
Fifteen of the dead have so far been identified as non-combatants and 27 as pro-government fighters, the Observatory said. Around 15 Isis fighters were also killed.
While there are reports several government positions were captured and fighting is still ongoing, Syrian state television said that the regime gunmen managed to repel the attack and launched a counteroffensive in the form of air strikes.
"Dozens of people are also missing, but it is not clear if they were kidnapped by Daesh,” said the Observatory’s chief Rami Abdurrahman, using an Arabic acronym to refer to the group. He said Isis deployed snipers on roofs of some buildings in Aqareb al-Safi.
At least two more civilians were injured in Isis shelling in the nearby town of Salamiyeh.
Isis, meanwhile, claimed via its news channel Amaq it had killed 100 government troops and captured two villages in Thursday's violence.
The militant organisation now controls just a fraction of the territory it held at the peak of its power in 2015, but it is still capable of inflicting death and destruction around the country.
Government forces are mainly on the offensive against Isis in the country's north. US-backed Kurdish troops are also closing in on the jihadists' de facto capital of Raqqa.
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