The projectiles were spillover from the fighting near Syria's disputed border with Israel, the army said.
Syria's military later said in a statement that Israel had attacked one of its military posts in support of terrorist groups, as it describes the jihadist rebels it is fighting in that area.
On Saturday, the Israeli Air Force attacked the Syrian government forces' tanks and artillery positions after 10 projectiles fell on the Israeli-controlled part of the Golan Heights.
Meanwhile, farmers and civilians were ordered to stay away from the Valley of Tears, New Quneitra, and open areas. No injuries or damage were reported.
Israel bombed Syrian targets in retaliation to Syrian mortar fire, acting on its long-standing promise to respond to every incident - intentional or not. "We will react with force to any firing on our territory", Prime Minister Benjamin Netanyahu said.
Amid heavy fighting between Syrian army forces and militias loyal to the regime of Bashar al-Assad and between rebel forces, mortar and tank shells spilled over onto the Israeli side of the border for a second day running.
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"We are not willing to accept any "drizzle" [of fire] or "spillover" on any front".
"We will respond strongly, resolutely and with levelheadedness to any such case", he said.
Israeli Defence Minister Avigdor Lieberman threatened to destroy Syrian air defense systems in March, after Damascus fired ground-to-air missiles at Israeli warplanes carrying out strikes.
Israel seized 1,200 square km of the Golan from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the worldwide community.
Israel captured the Golan Heights from Syria in the 1967 Mideast war.