Theodore McCarrick, the former archbishop of Washington, was removed from the ministry in June after a review board found there was "credible" evidence that he had assaulted the teen while working as a priest in New York in the early 1970s.
"Yesterday evening the Holy Father received the letter in which Cardinal Theodore McCarrick, Archbishop Emeritus of Washington (U.S.A.), presented his resignation as a member of the College of Cardinals," the Vatican said in a statement Saturday.
"Pope Francis accepted his resignation from the cardinalate and has ordered his suspension from the exercise of any public ministry, together with the obligation to remain in a house yet to be indicated to him, for a life of prayer and penance until the accusations made against him are examined in a regular canonical trial."
McCarrick, 88, is one of the most prominent American cardinals active on the international stage and the charges make him one of the most high-profile Catholic leaders to face abuse claims.
Although he has officially retired, McCarrick has continued to travel abroad regularly, including to defend human rights issues.
McCarrick was ordained a priest in 1958 and rose through the ranks in the Archdiocese of New York before being installed as archbishop of Washington in 2001, a post he held until 2006.
The claims against him were made public in June by Cardinal Timothy Dolan, the current archbishop of New York.
Dolan said an independent forensic agency "thoroughly investigated" the allegation.
A review board that included jurists, law enforcement experts, parents, psychologists, a priest and a religious sister then "found the allegations credible and substantiated" and the Vatican ordered McCarrick to stop exercising his priestly ministry.
At the time, McCarrick released a statement maintaining his innocence but added that he "fully cooperated" in the investigation.
Senior US church officials said they had received three allegations of McCarrick's sexual misconduct with adults decades ago, two of which resulted in settlements.
The US Catholic website Crux quoted a man as accusing him of abusing him in New York's St Patrick's Cathedral when he was a 16-year-old in the 1970s.
McCarrick remains a priest pending the Vatican investigative process which could see him excluded from the Church.
Yet the loss of his status as cardinal is in itself the rarest of moves.
The only previous such case came in 1927, when Pope Pius XI accepted the resignation of French cardinal Lois Billot, who had himself renounced his status for political reasons.
In March 2015, Pope Francis formally accepted the resignation of Keith O'Brien, but allowed him to keep the title of cardinal after the former Bishop of Edinburgh and former leader of the Roman Catholic church in Scotland resigned two years over allegations of inappropriate sexual behaviour towards priests in the 1980s.
Cardinals act as close papal advisors and can attend conclaves to elect new pontiffs if they are aged below 80.
Other cardinals caught up in scandal include Australia's top Catholic George Pell, number three in the Vatican. Pell faces prosecution in Australia for historical child sexual offences. He has pleaded not guilty to the charges.
The Archbishop of Santiago, Cardinal Ricardo Ezzati, was meanwhile summoned by the regional prosecutor's office at Rancagua, central Chile, to respond on August 21st to accusations of being involved in covering up sexual abuse by Chilean priests, 14 of whom were defrocked in May.