It was led by the Church of Scotland moderator at Edinburgh's St Giles' Cathedral.
Rt Rev John Chalmers told the congregation – including Scotland's finance secretary, John Swinney, and Labour's shadow foreign secretary, Douglas Alexander – that there would be no quick fix.
He said: "The Church here and in congregations across the country is playing its part in making it a little easier to stretch out that hand of friendship to those who are our fellow Scots who did not support the side we supported.
"How we voted on one particular day does not define who we are.
John Swinney, Johann Lamont, Ruth Davidson
and Willie Rennie and Ian Baxter
"How we work together to put in place the democratic will of the Scottish people will be defining - both for us as individuals and for us we as we work to redefine our place within the United Kingdom."
Also at the service were Better Together leader Alistair Darling, Scottish secretary Alistair Carmichael and former Liberal leader Lord Steel.
Scottish Conservative leader Ruth Davidson, Labour leader Johann Lamont and Lib Dem leader Willie Rennie were also present.
The service was designed to be part of a process of reconciliation to help both Yes and No campaigns reunite in the best interests of Scotland.
Both sides exchanged heated words in the run-up to the September 18th vote.
Rt Rev John Chalmers wanted the country to put differences aside.
He added: "The untold energy of people who love Scotland and care about its future has been used up on opposite sides of this debate, now we have to find a way of harnessing all of that energy so that it can be used on the same side.
"When the late Jimmy Reid addressed the Upper Clyde Ship Builders in 1971 – as they staged their sit-in – he said to them, 'the world is watching us, and it is our responsibility to conduct ourselves with responsibility, and with dignity, and with maturity'.
"Actually he said quite a bit more than that! But we know what he meant and we know that his words are as poignant today as they were in 1971. The eyes of the world are on us, and it needs to see us conduct ourselves with responsibility, with dignity, and with maturity.
"Post-referendum there are those who are elated or at least relieved, and there are those who are desperately disappointed, 'gutted' is the description that I have frequently heard. Feelings like these will take time to heal and I want no one to think that I think that there is a quick fix or an easy dusting down.
"For some, this referendum has been about national identity; for us all it has been about self-identity and that is about as close to the soul as it gets.
"So recovery and healing is a soul-searching matter and for me, that is a deeply spiritual matter, so no quick fix.
"Instead, it will take a force of magnanimity and graciousness to restore equilibrium to both nation and individuals."
"Today, and in the weeks to come, Scotland needs magnanimity all round and it needs a process for shaping our future which allows every voice (the 45% as well as the 55%), not just to be heard but to be listened to."
The moderator has also asked the Kirk's 800 ministers to join his call for unity.