At his weekly blessing, Francis referred to a statement by the Latin Patriarchate of Jerusalem, the Catholic authority in the Holy Land, about an incident on Saturday.
The Patriarchate said an Israel Defence Forces (IDF) sniper killed the two women, whom the pope named as Nahida Khalil Anton and her daughter Samar, as they walked to a convent of nuns in the compound of the Holy Family Parish.
The Patriarchate statement said seven other people were shot and wounded as they tried to protect others.
"I continue to receive very grave and painful news from Gaza," Francis said. "Unarmed civilians are the objects of bombings and shootings. And this happened even inside the Holy Family parish complex, where there are no terrorists, but families, children, people who are sick or disabled, nuns."
Francis also referred to the Patriarchate's statement that a convent of nuns of the order founded by Mother Teresa was damaged by Israeli tank fire.
"Some would say 'It is war. It is terrorism.' Yes, it is war. It is terrorism," he said.
An Israeli Foreign Ministry spokesperson said the incident was still under review and had no immediate comment on the pope's words.
The Israeli military said that church representatives had contacted it early on Saturday regarding explosions in the area but did not report any casualties in the church complex.
"The IDF only targets terrorists and terror infrastructure and does not target civilians, no matter their religion," the military said.
The pope's remarks on Sunday marked the second time in less than a month that he used the word "terrorism" while speaking of events in Gaza.
On November 22, after meeting separately with Israeli relatives of hostages held by Hamas and with Palestinians who have family in Gaza, he said: "This is what wars do. But here we have gone beyond wars. This is not war. This is terrorism."
Later that day, a messy dispute broke out over whether he used the word "genocide" to describe events in Gaza, with Palestinians who met him insisting that he did and the Vatican saying he did not.
Jewish groups criticised the pope for last month's "terrorism" comments.
Meanwhile Israel stepped up its bombardment of Gaza over the past 24 hours, killing at least 40 people, Palestinians said, after Israeli Prime Minister Benjamin Netanyahu argued the only way to secure the release of hostages was intense military pressure on Hamas.
