"Give rise to their souls," the priest intoned and let them rest "where there is no pain, sorrow or suffering."
After the prayers, Gilbert explained to the seven women who attended that God does not prevent evil acts, because he "chose to create us free."
People usually respond to tragedies such as the bombings with love, he said, exemplifying God's love for his creations.
Mary Tolokan, a substitute violinist with the Utah Symphony, was among those praying at the cathedral.
"I was shocked at the news," Tolokan said. "I texted my friend who ran in the marathon and finally heard this morning that she was fine. I was so relieved."
Gilbert also has a personal connection to Boston: His 21-year-old son, Aaron, is an undergraduate at Hellenic College in Brookline, Mass., which is part of the church's Holy Cross Greek Orthodox School of Theology.
The young man didn't go to the race, as he usually would, Gilbert said. He was studying.
But Gilbert's daughter, Christina, who lives in Chicago, graduated from the Greek Orthodox school and briefly was worried about her brother.
"She used to go the finish line to celebrate," the priest said.
At another time, he said, she could have been among the victims.
St. Mark's Cathedral hosted a special Mass on Tuesday night for those affected by the bombings.