O'Brien's resignation was welcomed by gay rights campaigners, who have been enraged by the 74-year-old Archbishop of Edinburgh's strident opposition to same-sex marriage.
As leader of Scotland's Catholics and Britain's only cardinal elector, his resignation means Britain will have no say in the choice of the next leader of the world's 1.2 billion Catholics.
Although he has not spoken publicly on the issue, it is understood that O'Brien continues to contest allegations from the 1980s that he made unwanted advances to four members of the clergy, including three current priests.
An investigation is under way into the claims, which resulted in one of the men requiring long-term psychological counselling.
O'Brien said the Pope had initially accepted his resignation last November but it was due to take effect to coincide with his 75th birthday next month. Cardinals under 80 are still entitled to attend the conclave to vote.
However, after weekend newspaper revelations, he said: "The Holy Father has now decided that my resignation will take effect today and that he will appoint an apostolic administrator to govern the archdiocese in my place until my successor as archbishop is appointed. I do not wish media attention in Rome to be focused on me - but rather on Pope Benedict XVI and on his successor."
- Independent