But, in a glowing letter of support, Francis makes clear that he accepted Wuerl's resignation reluctantly, at Wuerl's insistence, and that he believes Wuerl is not guilty of wrongdoing.
In a highly unusual move, Francis asked Wuerl, who keeps the title of cardinal, to stay on as administrator until another archbishop could be appointed. Usually the new bishop is announced at the same time of his predecessor's resignation, Presstv Reported.
Wuerl has been a key ally of Francis, defending the pontiff from attacks by conservatives in the Church, some of whom say the pope should resign over the sexual abuse crisis.
The Washington position is the most important and visible for the Church in the United States because of its proximity to national political power.
US Bishop Robert Barron said he was sure Wuerl had offered his resignation for the good of the church and that is also how Pope Francis would have seen it.
"This is about moving forward," said Vatican spokesman Greg Burke confirming the pope had accepted Wuerl's resignation.
Reuters correspondent Philip Pullella said critics of the Pope would be unhappy Wuerl will remain in an administrative position in the Washington diocese.
Wuerl, 77, has been under fire since the release in August of a US Grand Jury report on sexual abuse found evidence that at least 1,000 people, mostly children, had been sexually abused by some 300 clergymen over the course of 70 years.