Israeli security authorities gave the all-clear in the early hours of Sunday morning following Iran's major drone and missile attack.
The lifting of the alert means residents no longer need to stay close to air raid shelters.
Army spokesman Daniel Hagari said Tehran had launched about 200 drones and missiles during its unprecedented direct attack on Israel overnight, but most were intercepted.
There was slight damage to a military base, and a young girl was injured in southern Israel.
Israeli air raid sirens sounded across the country as the drones and missiles that hadn't already been shot down arrived over Israeli cities.
Iran said it had targeted Israel in retaliation for a suspected Israeli attack on an Iranian embassy compound in Syria earlier this month which killed two brigadier generals and five other members of Iran's powerful Islamic Revolutionary Guards.
The tensions between the two arch-enemies have been heightened by the war in Gaza.