One rocket landed inside the courtyard of an Israeli kindergarten building.
No group claimed immediate responsibility, though the IDF holds Hamas, which controls Gaza, as responsible for all attacks from the coastal strip.
The alert sounded a few days after Hamas allegedly agreed not to fire rockets into Israel as part of a Palestinian unity plan.
No injuries were reported in the attack. It is the first rocket from Gaza in about two months.
The long-range Grad rockets were aimed at a crossing on the Israel-Egypt border, but landed in Egypt.
A rocket fired from the Gaza Strip exploded in a kibbutz near Gaza without causing casualties or damage.
At least two rockets fired from the Gaza Strip struck Israel on Wednesday, moments before a three-day truce was set to expire, police said.
Sirens warning of incoming rockets from Gaza went off in southern Israel on Wednesday, signaling a possible breakdown of a three-day truce about two hours before it was due to expire.
A Gaza truce was holding on Wednesday as Egyptian mediators pursued talks with Israeli and Palestinian representatives on an enduring end to a war that has devastated the Hamas Islamist- dominated enclave.
French and Indian TV stations broadcast footage showing Hamas rocket launching facilities in a civilian area.