The army said it had fired at three fighters after spotting them laying explosives on a path used by troops.
Farther south in Rafah's Tal Sultan refugee camp, a Palestinian teenager identified as Rizek Maslah, 16, was shot dead by Israeli soldiers near the border with Egypt.
All 21 Jewish settlements in the Gaza Strip are due to be cleared next year along with another four in the northern West Bank.
The latest deaths bring the overall toll since the September 2000 start of the Palestinian uprising to 4,659, including 3,614 Palestinians and 970 Israelis.