Seven people were seriously injured during the attack on Thursday evening when shrapnel ripped through the intended victim's home in Gaza's Rafah camp.
But Muhammad al-Khalil escaped with light injuries, though his 10-year-old son, Yasir, was seriously wounded.
The Israeli army has confirmed the number of casualties.
It was the second time Israel has tried to assassinate al-Khalil, whom it alleges heads Islamic Jihad's al-Quds Brigades in the southern Gaza Strip.
His house was blown up on 15 May in another Israeli helicopter missile attack, with a spokesman claiming at the time that his home was used to store weapons and make explosives.
Al-Khalil also had to have his foot amputated at the beginning of the al-Aqsa Intifada in September 2000 after he suffered major injuries in a rocket attack.
The assassination attempt may have been related to a Palestinian makeshift rocket attack on the southern Israeli town of Sderot, which missed the town and injured no-one.
In addition to the two home-made rockets on Sderot, the Israeli military also reports that a mortar also landed near the illegal Jewish colony of Morag in southern Gaza – again injuring nobody.
Israeli occupation forces have since closed down the checkpoints along the trans-Gaza highway and the Rafah border crossing with Egypt, in effect cutting Gaza into three parts.