“What would the Church be without you?” the Pope, himself a member of the Jesuit religious order, told the hundreds of nuns among the 3,000 worshippers in the cathedral’s pews.

Nuns in the pews began to smile as they absorbed Francis’ words, and the priests, brothers and lay people in the crowd turned to shake their hands and thank them as well.

“Women of strength. Fighters. With that spirit of courage which puts you in the front lines in the proclamation of the Gospel,” the Pope continued.

“To you religious women, sisters and mothers of this people, I wish to say ‘thank you,’ a big thank you, and to tell you that I love you very much.”

Then all in the cathedral rose to their feet, applauding for the nuns. It was a poignant moment of redemption for thousands of U.S. sisters who had been the subject of a Vatican investigation launched seven years ago under Francis’ predecessor, Pope Emeritus Benedict XVI.

Traditionalists within the Vatican had charged the Leadership Conference of Women Religious, a network of 1,500 Catholic sisters that represents about 80 per cent of the 50,000 nuns in the United States, with straying too far from doctrine and focusing too intently on social issues to the exclusion of others.

But soon after his election in March 2013, Francis signalled that America’s nuns need not fear the investigation. It came to a quiet end, without harsh consequences, last April.

“It’s probably one of the most wonderful affirmations of our religious vocation that we could have received,” Sr. Marguerite of the Little Sisters of the Poor community in the Bronx said after the service. “It was a surprise. I happened to be looking up when he made that gesture” of reaching out with his hand while thanking them.

Francis came to the 136-year-old St. Patrick’s Cathedral — gleaming thanks to an almost-completed $175-million facelift — on the second leg of his six-day visit to the United States, his first time in this country of 68 million Catholics. He had spent most of the day in Washington, D.C., where the day before he took time to praise another group of women religious, making an unscheduled stop at the Little Sisters of the Poor, a community of nuns who operate nursing homes and who are locked in a tense legal battle with the Obama administration over contraceptive coverage mandated by the president’s health care law.

At the evening prayer service on Thursday, he also acknowledged, for the second time on this trip, the clergy sex abuse scandal that has rocked the American Church.

“I know that, as a presbyterate” — referring to the priesthood — “in the midst of God’s people, you suffered greatly in the not distant past by having to bear the shame of some of your brothers who harmed and scandalized the Church in the most vulnerable of her members,” he said. He spoke in his native Spanish, and it was translated on screens attached to pillars throughout the cathedral.

“In the words of the Book of Revelation, I know well that you ‘have come forth from the great tribulation.’ … I accompany you at this time of pain and difficulty, and I thank God for your faithful service to His people.”

Francis’ words are unlikely to please victims’ advocates, who have voiced anger at what they see as his weak response to the crisis. Vatican officials say they expect the pontiff to meet with several victims at some point during the trip, but will not confirm that it will happen, or where.

At St. Patrick’s, celebration was on the minds of thousands of Catholics and other Francis fans who lined Fifth Avenue, a stretch of which had been closed to traffic near the neo-Gothic cathedral.

As he approached in the popemobile, their roar of welcome could be heard through the cathedral’s thick walls, and it spread to the 3,000 waiting inside — about half of whom were men and women religious — as the 78-year-old pontiff began his ascent of the cathedral’s steps and crossed the threshold through its bronze doors.

Before beginning his prepared remarks, Francis first addressed Muslims who were mourning the more than 700 people trampled to death Thursday during a pilgrimage in Mecca:

“My greetings as they celebrate the feast of sacrifice,” Francis said, referring to the holiday of Eid al-Adha. Then he expressed his “closeness in the face of tragedy, tragedy they suffered in Mecca.”

The vespers service had a strong New York flair to it, with Sen. Charles Schumer, Gov. Andrew Cuomo and New York City Mayor Bill de Blasio greeting Francis on the cathedral steps.

At the end of the service, an enthusiastic Cardinal Timothy Dolan told the Pope that when he walked through the doors of New York’s iconic cathedral, he became “an official” New Yorker. Francis smiled widely in response.

Dolan also thanked him for mentioning New Yorkers Thomas Merton and Dorothy Day — the theologian and writer, and the founder of the Catholic Worker Movement, respectively — in his speech to Congress earlier that day.

“Thanks for stopping by,” Dolan said in English. “Torna presto!” he added in Italian — “Come back soon!”

(With files from David Gibson.)

Read our complete coverage of the Pope's historic visit to the United States of America.