Romanelli was lightly injured.
The church has long been the centre of worship for Gaza’s Catholic minority.
During the war, it also became a place of refuge, sheltering hundreds of Palestinian civilians - Muslims as well as Christians.
Some 450 displaced people were reportedly sheltering at the site when it came under attack.
A man and a woman who were seriously injured in the midmorning strike died in surgery at nearby al-Ahly Hospital, according to the hospital’s director of surgery, Mostafa Naim.
Naim identified two of the dead as Foomya Ayad and Saad Eissa Salama. They were Orthodox Christians but were sheltering at the church, according to Kamel Ayad, a spokesman for Gaza’s Greek Orthodox Church.
The patriarchate later confirmed the death of a third person, Najwa Abu Daoud.
“The Latin Patriarchate strongly condemns this tragedy and this targeting of innocent civilians and of a sacred place,” it said in a statement. “However, this tragedy is not greater or more terrible than the many others that have befallen Gaza.”
It added: “The time has come for leaders to raise their voices and to do all what is necessary in order to stop this tragedy which is humanly and morally unjustified.”
The office of Prime Minister Benjamin Netanyahu said in a statement that Israel “deeply regrets that a stray ammunition hit Gaza’s Holy Family Church. Every innocent life lost is a tragedy. We share the grief of the families and the faithful.”
The Israel Defence Forces said an initial inquiry “suggests that fragments from a shell fired during operational activity in the area hit the church mistakenly”.
The IDF said it “directs its strikes solely at military targets and makes every feasible effort to mitigate harm to civilians and religious structures, and regrets any unintentional damage caused to them”.
Israel’s Foreign Ministry said the results of the military’s investigation would be “published transparently”.
Cardinal Pierbattista Pizzaballa, the Latin patriarch of Jerusalem, told Vatican News that a tank had fired on the church directly, “the IDF says by mistake, but we are not sure about this”.
Caritas, a Catholic charity that runs mental health services at the Holy Family Church, said the building’s roof was hit by a shell, scattering shrapnel across the courtyard below and severely wounding two elderly women sitting inside a Caritas tent, along with others nearby.
As shelling and Israeli military operations had picked up in the area over the past week, Romanelli had urged people sheltering at the church to stay inside. If most hadn’t heeded that warning, the casualty count today could have been much higher, the Caritas statement said.
Pope Leo XIV said in a statement that he was “deeply saddened” to learn of the attack and that “he assures the parish priest, Father Gabriele Romanelli, and the whole parish community of his spiritual closeness”.
The Pope reiterated his call for an immediate ceasefire in Gaza, according to the statement, which was signed by Cardinal Pietro Parolin, the Vatican secretary of state.
The strike on the Holy Family Church also drew swift condemnation from politicians in Italy, which surrounds Vatican City.
Italian Prime Minister Giorgia Meloni was one of the first to confirm the strike on the church.
She said in a statement in Italian: “The attacks against the civilian population that Israel has been carrying out for months are unacceptable. No military action can justify such behaviour.”
The Jerusalem patriarchate for the Greek Orthodox Church condemned the strike as “a flagrant violation of human dignity and a blatant violation of the sanctity of life and the sanctity of religious sites, which are supposed to provide a safe haven in times of war”.
The strike “destroyed large parts of the complex” and forced some people with special needs who rely on ventilators to evacuate the area, putting their lives at risk, the statement added.
An aid worker in contact with the church said they had provided the GPS co-ordinates for the entire church compound to the Israeli military early in the war.
Pope Francis was an early and outspoken critic of the way Israel has waged its war in Gaza, which Israel launched in retaliation for the Hamas-led attacks on southern Israel on Oct. 7, 2023, during which Palestinian militants killed about 1200 people - mostly civilians - and took about 250 hostages to Gaza.
The ensuing Israeli military campaign has devastated most of the Gaza Strip, displaced nearly all of its population at least once and killed more than 58,000 people.
The close attention from Pope Francis both made the church famous and drew attention to the plight of Gaza’s civilians as they tried to survive Israeli bombardment, repeated displacement and shortages of food, clean water, fuel and other basic supplies.
After an Israeli sniper killed two women who had taken shelter at the Holy Family Church in December 2023, two months into the war, Francis called Israel’s actions in Gaza “terrorism”.
Seven other people were injured in the shooting on the parish complex, the patriarchate in Jerusalem said at the time.