Wednesday's strike near the town of Khan Yunis followed a flare-up of Israeli-Palestinian violence on Tuesday, the latest since a ceasefire was declared in February.
The Israeli army said it targeted a mortar launcher that had just been fired and another that was about to be used, as well as a car loaded with mortars.
Witnesses said three fighters from the Islamic group Hamas fled as the missiles struck. No one was hurt.
An army spokeswoman said the aim of the strike was only to destroy the weapons.
Israeli forces killed a West Bank leader of Islamic Jihad on Tuesday, drawing vows of revenge. The army said he had planned to send bombers into the Jewish state.
A rocket and mortar barrage by fighters hours later killed two Palestinian farmers and a Chinese labourer working at a Jewish settlement in Gaza.
Hamas and Islamic Jihad are sworn to Israel's destruction. Both groups agreed to a de facto ceasefire in February at the behest of President Mahmoud Abbas. The truce has sharply reduced violence but has been prone to violations.
Israeli Prime Minister Ariel Sharon wants calm to prevail ahead of a planned removal of all 21 settlements in Gaza and four of 120 in the West Bank starting in mid-August.
Though polls show most Israelis support the pullout, Sharon's hardline opponents call it a "reward for Palestinian terrorism" and many settlers are vowing to resist eviction.