Cardinal Keith O'Brien's comments came as world leaders, both religious and political, praised the 85-year-old Pontiff following his momentous decision, which surprised even the Vatican hierarchy.
The cardinal said: "I was shocked and saddened to hear of the decision to resign. I know it has come after much prayer and reflection.
"I will offer my prayers for Pope Benedict and call on the Catholic community of Scotland to join me in praying for him at this time of deterioration in his health as he recognises his in-capacity to adequately fulfil the ministry entrusted to him."
First Minister Alex Salmond said the Pope's decision to step down because of advancing age was "selfless".
He said: "The Scottish Government holds the Holy See in the utmost respect and is aware Pope Benedict's decision will be a great shock to the Catholic community in Scotland and internationally.
"We should respect the decision of His Holiness to pass on his ministry in a selfless gesture, on health grounds, in the best interests of the Church.
"Like many Scots, I remember with great fondness the resounding success of Pope Benedict's visit to Scotland in 2010 and the Papal Mass celebrated at Bellahouston Park. I wish him a very peaceful retirement."
The Most Rev David Chillingworth, Bishop of St Andrews, Dunkeld and Dunblane and Primus of the Scottish Episcopal Church, said: "Christians of all traditions will have heard of the resignation of Pope Benedict XVI with regret.
"He has been a distinguished holder of his office, widely respected for his scholarship and his spirituality.
"Pope Benedict has made a difficult personal decision which shows the mark of a humble servant of Jesus Christ. We wish him a peaceful and holy retirement." News that the Pope was stepping down because of his age and infirmity were revealed in later editions of yesterday's Evening Times and immediately the most senior Catholic figures spoke of the Pontiff's "great courage" in making the announcement.
The Pope will resign on February 28, the first to do so in nearly 600 years.
The Most Rev Vincent Nichols, Archbishop of Westminster and leader of Catholics in England and Wales, said the announcement had "shocked and surprised" everyone.
"Yet, on reflection, I am sure that many will recognise it to be a decision of great courage and characteristic clarity of mind and action," he said.
"The Holy Father recognises the challenges facing the Church and that 'strength of mind and body are necessary' for his tasks of governing the Church and proclaiming the Gospel.
"I salute his courage and his decision."
Other tributes came from the two most senior clerics in the Church of England, the Most Rev Justin Welby, Archbishop of Canterbury, and Dr John Sentamu, Archbishop of York.
Archbishop Welby said the Pope had held his office "with great dignity, insight and courage".
He added: "I speak not only for myself, and my predecessors as archbishop, but for Anglicans around the world, in giving thanks to God for a priestly life utterly dedicated, in word and deed, in prayer and in costly service, to following Christ."
Prime Minister David Cameron, who met the Pope in London during his visit to Britain in 2010, said: "He has worked tirelessly to strengthen Britain's relations with the Holy See.
"His visit to Britain in 2010 is remembered with great respect and affection. He will be missed as a spiritual leader to millions."
Labour leader Ed Miliband said Pope Benedict had made a "brave" decision.
"Many people will remember his historic visit to the UK in 2010 – which was a very special moment for many, especially Catholics, across the country," he said.
"His decision to stand down is a brave one and we know he will not have reached it lightly."
Pope Benedict announced his decision in Latin during a meeting of Vatican cardinals.
He emphasised that carrying out the duties of being Pope requires "both strength of mind and body".
"After having repeatedly examined my conscience before God, I have come to the certainty that my strengths due to an advanced age are no longer suited to an adequate exercise of the Petrine ministry," he told the cardinals.