Witnesses said the helicopter fired at least one missile which badly damaged the home of Muhammad al-Shaikh Khalil.
Sources within the Islamic group confirmed to AFP Shaikh Khalil, who heads up its al-Quds Brigades military wing in the southern Gaza Strip, escaped unharmed.
The strike came just hours after Israeli helicopter gunships pounded targets in Gaza City in a failed attempt to eradicate the Islamic Jihad's top leader, Muhammad al-Hindi, who also escaped unharmed.
The assassination attempts came after a week in which 13 Israeli soldiers were killed in Gaza, most of them in two deadly attacks claimed by Islamic Jihad.
Elsewhere in Rafah, two Palestinians were injured when Israeli troops opened fire in Salah al-Din area, Palestinian medics told AFP, saying a 45-year-old man was in critical condition.
The two incidents occured just hours after troops withdrew from the flashpoint city on the border with Egypt.
Two soldiers were killed by Palestinian militants in Rafah on Friday.
The army said they were felled by sniper fire, but al-Aqsa Martyrs Brigades - an armed offshoot of Palestinian leader Yasir Arafat's Fatah movement - said they killed them in a roadside bombing.