Pope Benedict XVI accepted his resignation seven days ago but it was only made public today by the Church which released a statement by Britain’s most senior cleric.
The cardinal was expected to leave his post in three weeks times but his departure will only fuel the controversial surrounding his alleged behaviour. He added that he would not be attending the conclave of cardinals due to choose a successor to Pope Benedict next month in Rome, leaving Britain's Roman Catholics with no vote in the election.
In a prepared statement Cardinal O'Brien said he had lodged his resignation with the Vatican in November ahead of his 75th birthday on March 17.
He said: "The Holy Father has now decided that my resignation will take effect today, 25 February, 2013, and that he will appoint an Apostolic Administrator to govern the Archdiocese in my place until my successor as Archbishop is appointed.
"In the meantime I will give every assistance to the Apostolic Administrator and to our new Archbishop, once he is appointed, as I prepare to move into retirement.
“I have valued the opportunity of serving the people of Scotland and overseas in various ways since becoming a priest. Looking back over my years of ministry: For any good I have been able to do, I thank God."
And what could be seen as a direct comment on the row which has engulfed him in recent days the Cardinal added pointedly: "For any failures, I apologise to all whom I have offended."
He had been expected to be part of the conclave which is due to gather to chose the Pope’s successor but instead Cardinal O’Brien made plain he will be playing no part on the decision making process.
He said: "I also ask God’s blessing on my brother cardinals who will soon gather in Rome to elect his successor. I will not join them for this conclave in person.
"I do not wish media attention in Rome to be focused on me – but rather on Pope Benedict XVI and on his successor. However, I will pray with them and for them that, enlightened by the Holy Spirit, they will make the correct choice for the future good of the Church."
Cardinal O’Brien who has strenuously denied acting improperly has been Scotland’s Roman Catholic leader since 1985 and has been an outspoken critic on same-sex marriage legislation.