
The Islamic State of Iran and Syria (ISIS) regard Christian as infidels. The religious uprisings and persecution from the militants has forced many Christian communities from their homes in Syria and northern Iraq.
Al-Qaryatain was captured in the militants' first major offensive since May, when they seized the historic town of Palmyra, famed for its Roman-style ruins.
More than 230,000 Syrians have died in the civil war, which began after anti-government protests in March 2011.
Rebel groups that originally fought against the government of President Bashar al-Assad have also been battling each other in an increasingly complex and bloody conflict.
Separately on Friday, Prime Minister Netanyahu accused Iran of giving "sponsorship and instruction" to militants who fired rockets on Israel.
An Israeli defence official earlier revealed that at least five or six Palestinian militants from the Islamic Jihad group had been killed in an Israeli attack, in retaliation for the rocket fire.
However, a Syrian army source, quoted on Syrian state TV, said the Israeli strike - on a car near the town of Quneitra - had killed five civilians.
One Syrian soldier was earlier reported killed in an Israeli strike on military positions in the Syrian-held section of the Golan Heights.
Israel seized most of the Golan Heights from Syria in the closing stages of the 1967 Six-Day War.