On Sunday, the IDF told residents of five Syrian villages inside the zone to stay in their homes until further notice.
The Golan Heights is a rocky plateau about 60km (40 miles) south-west of Damascus.
Israel seized the Golan from Syria in the closing stages of the 1967 Six-Day War and unilaterally annexed it in 1981. The move was not recognised internationally, although the US did so unilaterally in 2019.
The Israeli move in the buffer zone came after Syrian rebel fighters captured the capital, Damascus, and toppled Bashar al-Assad’s regime. He and his father had been in power in the country since 1971.
Forces led by the Islamist opposition group Hayat Tahrir al-Sham (HTS) entered Damascus in the early hours of Sunday morning, before appearing on state television to declare Syria to now be “free”.
Netanyahu said the collapse of the Assad regime was a “historic day in the Middle East”.
“The collapse of the Assad regime, the tyranny in Damascus, offers great opportunity but also is fraught with significant dangers,” he said.
He said events in Syria had been the result of Israeli strikes against Iran and the Iran-backed Lebanese armed group Hezbollah, Assad’s allies, and insisted Israel would “send a hand of peace” to Syrians who wanted to live in peace with Israel.
The IDF seizure of Syrian positions in the buffer zone was a “temporary defensive position until a suitable arrangement is found”, he said.
“If we can establish neighbourly relations and peaceful relations with the new forces emerging in Syria, that’s our desire. But if we do not, we will do whatever it takes to defend the State of Israel and the border of Israel,” he said.