A ministry statement said another Palestinian was injured in the raid that targeted Khan Younis south of Gaza City.
The new fatality brought the death toll from Israeli airstrikes in the Gaza Strip to 11 and 80 others injured since Friday.
Tension escalated across the Palestinian territories on Monday when Israeli forces detained Bassam al-Saadi, a senior leader of the Islamic Jihad group, in a raid in the West Bank city of Jenin.
The Israeli army has imposed restrictions on the Gaza Strip, including the closure of border crossings with the Palestinian territory, amid fears of a retaliatory response from the Islamic Jihad group to the arrest.
The Palestinian group said senior leader Tayseer al-Jabari was among those killed in Israeli attacks on Gaza on Friday.