One of them was identified as Islam al-Wadiya, 24, who was killed on Thursday at an army checkpoint to the east of Gaza City.
Israeli military sources had earlier said that they shot and "apparently killed" two figures who were spotted crawling near the post.
Wail Dahduh, Alajzeera's correspondent from Gaza, said the two Palestinians, who belonged respectively to the al-Aqsa Martyrs Brigades and al-Quds Brigades, were killed in a joint operation near Nahal Uz crossing, east of al-Shujaiya neighbourhood in Gaza City, as they attempted to enter a nearby military site.
Funerals of fighters are almost a
daily feature of life in Gaza City
Armed clashes have erupted in many other areas in Gaza, he added.
In another incident, an Israeli man was killed in an explosion in the Rafah region of the southern Gaza Strip, Israeli security sources said.
There was no immediate confirmation of the victim's identity, but sources within the resistance group Hamas earlier claimed to have launched an attack on a tank unit in the area, which borders Egypt.