The incursion drew heavy fire from Palestinian fighters.
An Israeli army spokeswoman confirmed that forces had operated in Gaza and had come under gun and mortar fire.
The incursion comes after two Hamas fighters were killed in an overnight Israeli air raid in southern Gaza, and two days after Palestinian fighters carried out a cross-border raid in which two Israelis were killed.
The two Palestinians killed in Thursday's raid near the town of Khan Younis were named as cousins Mohammed and Amil Al Najaf, both members of Hamas's armed wing, the Ezzedin al-Qassam Brigades.
Olmert warning
Ehud Olmert, the Israeli prime minister, has vowed to "keep hitting Hamas" and end attacks from Gaza in the wake of Wednesday's raid by Palestinian fighters on a fuel terminal in Israel.
He blamed Hamas, which governs the Gaza Strip, for the attack.
"Hamas today runs the Gaza Strip, and this organisation and all its members bear responsibility for the incessant terror and it will have to bear the inevitable price for its actions," Olmert said on Thursday.
Two Israeli civilians and two Palestinian fighters were killed in an exchange of fire after the Palestinians stormed the Nahal Oz crossing, which is mainly used for the transit of fuel.
At least three Palestinians were later killed in Gaza after Israeli shelling hit a house in al-Shegaeya area of Gaza City.
Palestinians have protested against Israel's temporary shutdown of the terminal which is Gaza's only source of fuel.