The Rev. Mary-Marguerite Kohn, 62, died Saturday night at the University of Maryland Shock Trauma Center of injuries sustained Thursday in a double shooting at St. Peter's Episcopal Church in Ellicott City, police said Sunday.
Kohn was co-rector of the Howard County church.
The second woman, church employee Brenda Brewington, 59, died Thursday.
Kohn had been on life support at the Maryland Shock Trauma Center since Thursday.
Police said they had taken Kohn's body to the state medical examiner's office for an autopsy. The church said in a statement that her family planned to donate her organs.
Howard County police said the suspected shooter, Douglas Franklin Jones, 56, was found in the woods nearby, dead of a self-inflicted gunshot wound.
In a statement, the church said Jones, a homeless man whom the church fed frequently, became angry last week about being told to limit his visits to the food pantry. The church said a custodian found Kohn and Brewington in an office Thursday, suffering from gunshot wounds.
"The assailant, a homeless man who was receiving food from St. Peter's pantry on a regular basis, had become belligerent when told that, pursuant to standard policy, the church would have to limit his visits to preserve supplies," the statement said.
St. Peter's warden, Craig Stuart-Paul, described Kohn as "one of the kindest, most giving people I have ever known. She never turned away a person in need, and even in death she is bringing life through the donation of her organs. I just hope that some of her amazing spirit goes along with them."
A shaken and stunned congregation came together for a service Sunday at the church, located in the 3600 block of Rogers Avenue, near Ellicott City's historic downtown.
For two hours, parishioners prayed and mourned the two women, and vowed that their contributions would not be forgotten.
"The Episcopal Church is in pain and agony today," said the Rev. Eugene Taylor Sutton, bishop of the Episcopal Diocese of Maryland. "Two wonderful women have been slain in this place."
The Rev. Kirk Alan Kubicek, the church's remaining rector, also spoke to the roughly 175 parishioners gathered at the church, which was founded in 1842.
"No times have ever seemed so bad as these past few days," he said, adding that the "badness" lasted only seconds "and yet seems to have eternal, everlasting consequences for us all."
Sutton spoke about anger at a society "that has still not figured out how to keep guns out of the hands of those with mental illness."
He acknowledged anger, too, toward Jones but also said the man was himself a victim.
"We are followers of Christ, and so the process of forgiveness has already begun," Sutton said.
Kohn's funeral will be held at 3 p.m. May 8 at the Cathedral of the Incarnation in Baltimore, according to an announcement made Sunday in church. Services for Brewington will be held at 1:30 p.m. May 10 at St. John's Episcopal Church in Ellicott City.