It marked the most serious confrontation yet in Syria between Israel and Iranian and Iran-backed forces that have established a major foothold in the country while fighting in support of President Bashar Assad in the civil war.
Israel said the F-16 crashed during a mission to strike Iranian drone installations in Syria. It said it sent its jets into Syria after shooting down an Iranian drone over Israeli territory earlier on Saturday.
The military alliance fighting in support of Assad denied any of its drones had entered Israeli air space. In a statement, it said Israel had targeted an air base in the Homs desert that is being used to fly drones in missions against Islamic State.