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The special Mass, held under the gaze of a large, specially-installed portrait of the retiring pontiff, was led by Bishop Gerald Walsh in the absence of Cardinal Timothy Dolan, who went to Rome for the conclave to choose the new pope.
Benedict was the first pope to resign in 700 years, ending a turbulent eight-year reign often overshadowed by Vatican infighting and a raft of sex abuse scandals.
Under the neo-Gothic arches of the biggest Catholic cathedral in the United States, the bishop called for prayers for Benedict, to celebrate "his whole life" of service to the Church.
Walsh also called for prayers for the cardinals tasked with designating his successor, "their most sacred and important duty," and for the next pope, who will be faced with "many challenges," including "the rise of secularism all over the world."
Among the audience was Helen Sawyer, a woman in her 60s, who said she was "very sad" about the departure of "a wonderful man."
But she had a very particular idea of who should take on the mantle next: "somebody who has some of John Paul II, some of this pope, and maybe a little of Cardinal Dolan," she said.
Jose Aldaz, pianist and usher at the cathedral, said he came to "show support for the church and solidarity" on this historic day.
Liz Wetherall, 48, who attends daily Mass, said she had the "utmost respect" for a pope who retired because he didn't feel strong enough to continue.
She would like to see the Catholic hierarchy "be a little bit more liberal," she said. "But I don't see that happening," she added with a laugh.
According to a survey published last week by the Pew Research Center, 58 percent of American Catholics said, among other reforms, they were in favour of allowing priests to marry.
Many of those at Saint Patrick's yesterday talked about how, in this transition period and under a new pope, the Church could, as Wetherall termed it, "adapt to modern times, new problems."
Marketing consultant Mora Ryan agreed.
"I guess I would like to see some changes in the church on their views on sexuality, women, marriage," she said.
"But I think that will come in time."
