The penitential purple vestments of concelebrants Bishop Stephen Robson and Monsignor Michael Regan assumed a more meaningful hue for the congregation as they learned, some for the first time, the Cardinal would not be there to lead them in celebrating Pope Benedict XVI's eighth year as Pontiff because of the allegations against him.
Muted gasps of shock and surprise rippled around the large Cathedral space.
As the Mass began, the minor-key German air Out Of The Depths I Cry, Lord, To Thee was played on the cathedral organ.
Intended as an invocation to prayer for the German Pope Benedict as he faced his own agony miles away in Rome, it also helped heighten sensitivity to the Cardinal's personal plight somewhat closer to home.
But as the service progressed, it became clear stoicism would take over. In his final blessing Bishop Robson asked the faithful to keep to their Lenten intentions of praying for the Holy Father and his successor, and also for the Cardinal.
The Recessional hymn, to the rousing tune of Faith of our Fathers, was sung strongly and loudly: God Bless Our Pope, the great, the good.
Nevertheless, there were many shocked faces as the congregation filed out of the unusually long 90-minute mass.
Sir Tom Farmer, founder of Kwik Fit, a leading lay Catholic and a friend of the Cardinal for almost 40 years, said he was "quite surprised" by the news, but added: "Nobody knows who the four are who made these allegations and why they have been made at this particular time. Until everybody knows the facts it would be unwise of me to say more. But I will say one thing for certain: Cardinal Keith O'Brien is a good man."
Many preferred not to say anything about the bombshell, but local businessman and parishioner Gerald Della-Porta, who attended the mass with friends, was cautious, curt and emphatic in his response. "I would say only this. Let whoever wants to throw the first stone go ahead."
Gudrun Smith, a parishioner for 30 years, pointed out the Cardinal was well-loved and popular, and he was an "inspirational man".
"It's terribly sad whenever anything like this happens and there is a sense of sadness and shock, because many people hadn't heard about this before they came out to Mass."
Asked if she felt her faith had been shaken, she replied: "We are all being tested by this, but then these are testing times for all Christians.
"Monsignor Regan has always been very helpful to me and I will be guided by him."
Her friend Jonathan Jamal made it clear his view was equally supportive of the Cardinal. "We are all sinners before the cross of Christ," he said.
Although he missed celebrating Mass in public yesterday, it seems likely Cardinal O'Brien would have attended a private service in the little Byzantine-style chapel of St Bennet's in the grounds of his official archdiocesean residence in Morningside.
The peaceful location and beautiful surroundings of this sacred space will have offered him sanctuary as it has to his predecessors over the years.
As the congregation dispersed after Mass and left his beloved Cathedral empty, it was in that quiet place that the badly shaken Cardinal was understood to be praying and meditating yesterday, while also seeking the guidance of his closest advisors.
He remained there all day, unseen by the public but under the unblinking gaze of a statue of Our Lady.
The next step in his troubled spiritual journey was only just beginning.