The victims were among three killed in the strike, which wounded ten others and damaged parts of the compound.
According to church officials, the shell landed in an area sheltering displaced civilians, including children with disabilities. Parish priest Gabriel Romanelli was among the injured.
Israel issued a rare apology and said it was investigating the incident.
Pope Leo XIV renewed his call for a ceasefire, expressing sorrow and solidarity with Gaza’s Christian community and those affected by the ongoing conflict.