The drone was intercepted by a Patriot missile in the demilitarised zone between the Israeli- and Syrian-controlled parts of the Golan, a military spokeswoman said in a statement.
Israel and Syria are still technically at war, though the armistice line on the Golan Heights had remained largely quiet for decades until civil war erupted in Syria in 2011.
Israel seized 1,200 square kilometres of the Golan Heights from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the international community.
Israel has also seen regular spillover fire from the Syrian conflict and acknowledges carrying out dozens of air strikes to stop advanced arms deliveries to its arch-foe Hezbollah.
The Lebanese militant group is a key backer of Syrian President Bashar al-Assad and has fought alongside his troops against rebel forces.