Spokesperson Ashraf al-Qidra said that Nour Rasmi Hassan, five months pregnant when she died, and her daughter, Rahaf Yahya Hassan, were killed in the air strike, and three others injured.
Their house collapsed when Israeli jets struck a nearby building, close to the al-Maslakh Mosque in southern Gaza City.
The Israeli army said in a statement that the air strikes targeted "two Hamas weapon manufacturing facilities in the northern Gaza Strip."
The statement made no mention of any deaths or damage to civilian homes.
The strikes were carried out to retaliate a rocket fired from the blockaded coastal enclave late on Saturday night.
The rocket was destroyed by Israel's "Iron Dome" defense system south of Ashkelon, with no injuries reported.
The rocket followed further violence in the Gaza Strip, where Israeli forces shot dead two Palestinian boys, aged 13 and 15, at a rally east of Khan Younis on Saturday.
The mother and her daughter's deaths brings the total number of Palestinians killed in the Gaza Strip to nine since Friday.
As tensions have spiraled in recent weeks, several rockets have been fired from the blockaded coastal territory into southern Israel, with Israel's army launching retaliatory air strikes in nearly every case.
Although much of the rocket fire has been claimed by small militant groups operating in Gaza, the Israeli army has consistently held the territory's de facto leaders Hamas responsible.
Israeli army spokesperson Peter Lerner said on Sunday that Israeli forces held Hamas responsible for any "act of aggression" from the Gaza Strip.
"This weekend we have seen clear incitement encouraging the breach of Israel's sovereignty, violent confrontation against Israelis and threatening the residence of southern Israel," he said.
He added that Israeli forces would "continue to act, preempt and defeat those that plot to harm the civilians of Israel."