Cardinal Keith O'Brien said he had announced in November that he was planning to resign ahead of his 75th birthday in March in view of his "indifferent health".
"The Holy Father has now decided that my resignation will take effect today, 25 February 2013," the 74-year-old cardinal said and informed that he will not attend the papal conclave in Rome this week to elect Pope Benedict's replacement, leaving Britain unrepresented in the election.
O'Brien, who had also skipped Sunday mass at St. Mary's Cathedral in Edinburgh, had been due to fly out to the Vatican tomorrow for the long conclave to choose the new Pope.
Pope Benedict, who steps down on Thursday, has accepted the resignation as Archbishop of St. Andrews and Edinburgh, O'Brien, the leader of the Catholic Church in Scotland, said in a statement.
He said the pontiff would appoint an apostolic administrator to govern the archdiocese in his place until his successor is appointed.
"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. For any failures, I apologise to all whom I have offended," O'Brien said.
"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," the 74-year-old cardinal said in the statement.
The resignation of O'Brien comes in the wake of a report in Britain's Observer newspaper which had disclosed a series of allegations of inappropriate behaviour by three priests one former priest dating back to the 1980s.
O'Brien has denied the allegations and was expected to continue in his post until mid-March, when he was due to retire at age 75.
He has been an outspoken critic of gay rights, denouncing plans for the legalisation of same-sex marriage in the UK as "harmful to the physical, mental and spiritual wellbeing of those involved".
The papal conclave in Rome is already expected to be difficult in the circumstances created by Pope Benedict's unprecedented resignation.
The Vatican is also struggling to deal with reports of internal corruption and mismanagement.
London: Britain's senior-most Roman Catholic cleric resigned on Monday after being accused of "inappropriate acts" towards fellow priests and said he would not take part in the election of the next Pope this week.
First Published: Monday, February 25, 2013, 19:11