An Israeli missile hit the car of Ismael al-Ismar, a leader of al-Quds Brigades in the city of Rafah, close to the Egyptian border.
Shortly afterwards, mortars were fired from northern Gaza into southern Israel. There were no injuries.
Violence between Israel and militants in Gaza has flared since a deadly attack on Israeli buses last week.
The Israeli military said its target in Wednesday's attack had been an activist implicated in weapons smuggling and militant operations in Egypt's Sinai region.Fragile 'truce'
The BBC's Yolande Knell in Jerusalem says these exchanges threaten to undermine the informal ceasefire agreement that was announced by an official from Hamas, which governs Gaza, late on Sunday.
This was joined by smaller militant groups.
Al-Quds Brigade is the armed wing of the Islamic Jihad organisation.
On Monday, the Popular Resistance Committees (PRC) - agreed to halt rocket fire against Israel as a "temporary" measure "for the sake of the Palestinian people".
Earlier, Israel's army radio reported that Israeli Prime Minister Benjamin Netanyahu's security cabinet had decided the military would stop its air strikes on Gaza if militants there halted their attacks.
Tensions rose rapidly after a series of shooting ambushes near the Red Sea resort of Eilat last Thursday, which killed eight Israelis.
The militants responsible are believed to have been Palestinians from Gaza who crossed from Egypt.
The leader of the PRC, which Israel blamed for the attack was among 15 Palestinians killed in subsequent air raids in Gaza.
Militant groups there responded by firing more than a hundred rockets and mortar shells at Israeli towns and cities. One man was killed.