The Israeli military released a statement saying its Iron Dome Aerial Defense System intercepted two of the projectiles.
The fire triggered sirens in the southern town of Netivot and communities in the area surrounding the Gaza Strip, where residents have been ordered to stay close to shelters and bomb-proof rooms since the escalation began on Tuesday.
Earlier on Thursday, the Israeli military and the Gaza's Islamic Jihad announced that an Egyptian-brokered cease-fire was agreed, ending three days of cross-border fire that claimed the lives of 34 Palestinians.
The violence was sparked by the killing of Islamic Jihad's senior commander Baha Abu al-Atta. A pair of Israeli airstrikes on his home in Gaza city killed him and his wife on Tuesday before dawn.
At least 450 retaliatory rockets, launched by Islamic Jihad militants, reached southern and central Israel, according to official army figures.