"The crossing points for people and goods, Erez and Kerem Shalom, have been closed until further notice except for humanitarian aid," an army spokeswoman said.
She said that the measure was taken after a rocket fired from Gaza hit the Eshkol area of southern Israel on Friday, without causing any casualties or damage.
Signup to our newsletter and follow us on Facebook and Twitter!
It was the first to strike Israeli territory since September 16, and the second since the end of the Jewish state's devastating 50-day war on Gaza militants.
A ceasefire agreed between Israel and Gaza's Hamas rulers took effect on August 26, ending a conflict that claimed 2,140 Palestinian lives and 73 on the Israeli side, most of them from the army.
Both sides are expected to resume talks soon in Cairo as part of an effort to keep the ceasefire in place.