The move came weeks after a Vatican investigation cleared DeMarzio of sexual abuse allegations.
DiMarzio is 77 years old, two years beyond the normal retirement age for bishops. He submitted his resignation when he turned 75 on June 16, 2019, as required by Canon Law.
That resignation was accepted Wednesday by Pope Francis.
"In the selection of Bishop Robert Brennan, the Holy Father has called upon a native New Yorker to return to lead the faithful of Brooklyn and Queens," DiMarzio said in a statement. "On behalf of the Diocese of Brooklyn, I welcome Bishop Brennan who I have known for many years, with confidence in his ability to lead our Catholic community and build upon the pastoral achievements we have made. It has truly been an honor to serve as Bishop of the Diocese of Brooklyn for 18 years."
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Two men had separately claimed DiMarzio abused them a half century ago, when he was a priest in New Jersey. He still faces civil lawsuits in those cases.
Brennan, 59, was born in the Bronx and raised in Lindenhurst, on Long Island. He attended Our Lady of Perpetual Help Catholic School in Lindenhurst and St. John the Baptist Diocesan High School in West Islip and earned a Bachelor of Science degree in mathematics and computer science from St. John's University in Queens.
"I came to know amazing people in the Diocese of Columbus and there is a tremendous sadness in leaving them behind," Brennan said. "As I prepare for a return to New York, I am ready and eager to embrace the people of Brooklyn and Queens as their pastor. Knowing we are loved by Jesus, we will strive to show others his face, bearing the Joy of the Gospel and the Splendor of Truth. In the end, that's what it is all about - in Columbus, Brooklyn, and around the world."
Cardinal Timothy Dolan, who as archbishop of New York is the responsible for both the Brooklyn and Rockville Centre dioceses, welcomed Brennan back home.
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"During my over 12 years as archbishop of New York, I have come to know him as a fine priest and bishop, a warm individual, and a good friend," Dolan said.
Dolan, who had appointed an outside firm to investigate DiMarzio, thanked the bishop for his "zeal and dedication" in leading the Brooklyn diocese for 18 years and said he would continue to be a source of wisdom for the New York church.
(The Associated Press contributed to this report)
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