The Israeli military added that the retaliatory strike was aimed at two tanks and a position where the projectiles were fired into Israel.
Israel retaliated against Syria over the weekend after ten projectiles from Syria landed in the Golan Heights, a popular Israeli tourist destination.
The military "targeted two artillery positions and an ammunitions truck belonging to the Syrian regime", after "errant fire" from Syria hit the Israeli-controlled Golan Heights for a second day, it said in a statement.
Meanwhile, farmers and civilians were ordered to stay away from the Valley of Tears, New Quneitra, and open areas.More news: Kvitova sends Wimbledon warning with Birmingham title
Israeli Prime Minister Benjamin Netanyahu on Sunday accused Iran of establishing a military presence in Syria and arming the Lebanon-based Shiite militia of Hezbollah. No injuries were reported.
Most mortars and gunfire on Israel from Syria have been accidental spillover from the country's years-long civil war.
Israel bombed Syrian targets in retaliation to Syrian mortar fire, acting on its long-standing promise to respond to every incident - intentional or not.
Syrian state media said a number of people were killed and, citing the Syrian military command, said five soldiers were wounded.More news: Uber searches for new CEO, Mayer among candidates
According to SANA, the battles in this region are between President Bashar Assad's army and the Nusra Front, a Salafist rebel group in Syria. "We will respond strongly to any firing at our territory", he stated.
"We have no intention of allowing the breech of our sovereignty and harming of our security to go unpassed", said Israeli Defense Minister Avigdor Lieberman.
Intense fighting has rocked the Quneitra province of Syria, adjacent to the Golan Heights, since rebels there launched an attack on Saturday.More news: US secure first win of America's Cup, trail New Zealand 4-1