The incident happened just hours after grieving and angry Palestinians buried three children killed in a botched attack the day before.
The attack has sparked a debate in Israel as to the effectiveness of air strikes that target militants but are taking a mounting toll on innocent Palestinians.
Meanwhile Palestinian militants have vowed revenge for the deaths of the civilians.
In the most recent attack Israeli aircraft targeted militants but hit a house in Khan Younis instead, killing a man and a woman and wounding at least 13 people, including five children.
The dead woman was Fatma Abdel Khader, 35. The man, visiting from Saudi Arabia, was identified as Zakaria Ahmed, 45.
The missile blew a hole in a wall of the one-story concrete block shack. A pool of blood covered part of the kitchen floor of the badly damaged house.
A witness said a car carrying Palestinian militants passed the house as the missile struck. The militants jumped from the car and ran into a nearby field, apparently unhurt.
A senior Israeli air force officer said the missile missed its target by several dozen metres.
Killings spark debate
Israel says its strikes are aimed at militants involved in daily rocket fire from Gaza against Israeli towns.
The high civilian toll is stirring a debate inside Israel, with critics saying the air strikes serve only to inflame militant passions.
Two five-year-old children and a 16-year-old youth were killed in an air strike on Wednesday.
In a passionate funeral procession a mother of one of the young victims collapsed in grief and an elderly man kissed a poster of his dead grandson as they buried their children.
A militant grabbed a microphone and asked the crowd, “Do you want a cease-fire?” and the mourners shouted back, “No!”
He was referring to a shaky February 2005 truce declared by major Palestinian militant groups, including Hamas, which earlier this year took over the Palestinian parliament and Cabinet.
Militant groups pledged to increase their rocket attacks against Israel, targeting the town of Sderot, just outside Gaza’s border fence.
Abu Qusai of the Al Aqsa Martyrs’ Brigades, linked to Fatah, said flatly, “We will not commit to the truce.” Referring to the deaths of civilians in earlier incidents, he added, “How can we hear the cries of these children, like the ones on the beach of Gaza, and stand idle?”
On June 9, eight Gaza beachgoers were killed in a beach blast Palestinians blamed on an Israeli artillery shell. Israel claimed it was not responsible.
The Israeli military said on Thursday that examination of another fragment removed from the body of a wounded Palestinian receiving treatment in Israel backed up that conclusion.