Khalid al-Dahduh, also known as Abu al-Walid, was killed on Wednesday when the vehicle in which he was travelling exploded in the strike.
He was the leader of the Al-Quds Brigades in the Gaza Strip.
There was no immediate comment from the Israeli military.
Islamic Jihad, which boycotted a Palestinian general election last January in which its larger rival Hamas won a massive victory, has been behind the last six bombings in Israel.
Al-Dahduh's death brings to 4969 the number of people killed since the outbreak of the Palestinian uprising in 2000. Most of the victims have been Palestinian.