Rt Revd Dr Bob Gillies was speaking after Bailey Gwynne was stabbed to death during his lunchbreak at Cults Academy (below), in the west of Aberdeen.
A pupil, also 16, has been charged over Bailey's death. The school is closed until Monday and counselling has been made available to the student affected.
Aberdeen Police has confirmed it is treating the incident as a murder investigation.
We can confirm that the Cults Academy incident is being treated as a Murder Investigation.— AberdeenPolice (@AberdeenPolice) October 28, 2015
Mr Gillies said: "Such dreadful events as this impact in the most terrible of ways upon so many people and upon so many families.
"My deepest grief is with all those whose lives have been changed for ever as a result of this death."
A candelit vigil will be held in Cults Parish Church at 8pm tonight. It's doors were also open yesterday for the community.
Revd Ewen Gilchrist, the vicar of the church and also a member of the chaplaincy team at Cults Academy, said: "People are left bewildered.
"Most of all, our prayers and our sympathy go out to Bailey's family. They must be devastated and horrified by all that has happened.
"We feel so helpless. And then we realised that the one thing we could do was to open our church doors, so that people could come here to sit, or to pray, or to be listened to, or to be with their friends.
"It's a safe place, it's a sanctuary. It's the least we could do."
Dr Glen Reynolds, from the Catholic Archdiocese of Aberdeen, told Premier's News Hour: "It's shocked the entire community, not just in Aberdeen but in Scotland and throughout the UK, because it's so out of the ordinary. It's a very difficult time.
"In a situation like this people turn to their faith communities and their leaders and their counselling services because it's difficult not just to conceive the pain that people are going through but it's difficult to conceive why.
"We're all touched by this because each and every one of us surely appreciates that 'There but for the grace of God go I', and unfortunately for Bailey Gwynne what happened to him happened.
"It is a time when we reflect on not just our own mortality but we reflect on the fact that there's a very basic humanity to each and every one of us, which causes us to extend our thoughts and prayers to each and every one of us who might be a complete stranger but are now united in this collective grief."
Listen to Premier's Antony Bushfield speaking to Dr Glen Reynolds on the News Hour: