"We must be people of reconciliation, not revenge," he said. "The crimes of two young men must not be the justification for prejudice against Muslims or against immigrants."
Kelly McKernan, who lives just a few blocks from the bombing site, was crying as she stood outside the cathedral, where people were hugging on the sidewalk.
"I hope we can all heal and move forward," she said. "And obviously, the Mass today was a first step for us in that direction."
Because it is located within the bombing crime scene, Boston's historic Trinity Episcopal Church could not host services on Sunday. But the congregation was invited by Temple Israel to worship at their synagogue instead.
The FBI allowed church officials to enter the darkened church Saturday to gather the priests' robes and the wine and bread.
The temple isn't far from the hospital where the younger bombing suspect was being treated.
At least one man wore his blue Boston Marathon jacket with its gold unicorn symbol embroidered on the back.
"It's just really great to have a space that's safe and open and there's light," said Jonathan Ralton, who was volunteering handing out medals and Mylar capes after runners crossed the finish line last week. "You know, God is here. God is with us, wherever we gather. And so I'm just grateful that we have a place to gather and can celebrate."
At the synagogue, Trinity's Rev. Samuel T. Lloyd III offered a prayer for "those who must rebuild their lives without the legs that they ran and walked on last week."
"So where is God when the terrorists do their work?" Lloyd asked. "God is there, holding us and sustaining us. God is in the pain the victims are suffering, and the healing that will go on. God is with us as we try still to build a just world: a world where there will not be terrorists doing their terrible damage."
Associated Press writer Allen G. Breed contributed to this report.