"The aircraft of the Israeli enemy launches a number of missiles at several army positions" in Quneitra, causing material damage, it said.
Israeli Prime Minister Benjamin Netanyahu is set to meet with Russian President Vladimir Putin on Wednesday.
Earlier in the day, the Israeli Defence Force confirmed it shot down a Syrian drone which had entered its airspace.
According to SANA, the Israeli air strike was delivered at military positions near the settlements of Hodor, Tell Kurum and Jbaa.
The drone "infiltrated the Israeli border from Syria", the Israeli military statement said, without immediately elaborating on whether the shoot-down took place over the Golan.
The group of more than 40 mothers and children that crossed over in the pre-dawn hours of Wednesday were among the 3,000 Syrians who Israel says have received separate treatment in what it calls "Operation Doctor's Appointment". Israel worries Assad could let his Iranian allies entrench near its lines or that Syrian forces may defy a 1974 Golan demilitarization.
The air force has struck many targets it describes as Iranian deployments or arms transfers to Iran supported Hezbollah.
This is Netanyahu's third meeting with Putin this year and the ninth since 2015 when Russian Federation began supporting the Syrian government militarily against rebels. We will not allow Iran's entrenchment in Syria and we will not allow Syrian soil to be turned into a vanguard against the State of Israel.
"We made a decision to bring with us two wonderful children who are bravely fighting cancer: Mika, whom my wife and I have known for nine years, and Alon, whose parents emigrated from Russian Federation and who likes soccer very much".
But on Tuesday, Israel also signalled openness to eventual ties with Syria under Assad, a tacit acknowledgement that he was re-consolidating power as he beats back the rebels.
Under Assad family rule, Syria held direct negotiations with Israel in the United States in 2000 and indirect talks mediated by Turkey in 2008.